diff --git a/build.gradle.kts b/build.gradle.kts
index cb4eb4449..44cb3be69 100644
--- a/build.gradle.kts
+++ b/build.gradle.kts
@@ -134,7 +134,7 @@ val toObfuscate: Configuration by configurations.creating {
 val obfuscationLibs: Configuration by configurations.creating
 
 
-val mixcrAlgoVersion = "4.6.0-43-fixes"
+val mixcrAlgoVersion = "4.6.0-46-reduceToCommonAssembleFeature"
 // may be blank (will be inherited from mixcr-algo)
 val milibVersion = ""
 // may be blank (will be inherited from mixcr-algo or milib)
diff --git a/regression/cli-help/findAlleles.txt b/regression/cli-help/findAlleles.txt
index 8f5ede458..510265f3d 100644
--- a/regression/cli-help/findAlleles.txt
+++ b/regression/cli-help/findAlleles.txt
@@ -12,14 +12,13 @@ of V and J genes and the same features to align.
                              In case of directory no filter by file type will be applied.
       --output-template <template.clns>
                              Output template may contain {file_name} and {file_dir_path},
-                             outputs for '-o /output/folder/{file_name}_with_alleles.clns
-                               input_file.clns input_file2.clns' will be
-                               /output/folder/input_file_with_alleles.clns and
-                               /output/folder/input_file2_with_alleles.clns,
-                             outputs for '-o {file_dir_path}/{file_name}_with_alleles.clns
+                             outputs for '-o /output/folder/{file_name}_suffix.clns input_file.clns
+                               input_file2.clns' will be /output/folder/input_file_suffix.clns and
+                               /output/folder/input_file2_suffix.clns,
+                             outputs for '-o {file_dir_path}/{file_name}_suffix.clns
                                /some/folder1/input_file.clns /some/folder2/input_file2.clns' will
-                               be /seme/folder1/input_file_with_alleles.clns and
-                               /some/folder2/input_file2_with_alleles.clns
+                               be /seme/folder1/input_file_suffix.clns and
+                               /some/folder2/input_file2_suffix.clns
                              Resulted outputs must be uniq
       --no-clns-output       Command will not realign input clns files. Must be specified if
                                `--output-template` is omitted.
@@ -81,7 +80,7 @@ of V and J genes and the same features to align.
                                allele.
       --dont-remove-unused-genes
                              Don't remove genes that weren't used in clones in the result library
-  -O  <key=value>            Overrides default build SHM parameter values
+  -O  <key=value>            Overrides default find alleles parameter values
   -r, --report <path>        Report file (human readable version, see `-j / --json-report` for
                                machine readable report).
   -j, --json-report <path>   JSON formatted report file.
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAlign.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAlign.kt
index 5478babe8..508c8e637 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAlign.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAlign.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
@@ -73,9 +73,9 @@ import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
 import com.milaboratory.mixcr.cli.MiXCRCommand.OptionsOrder
 import com.milaboratory.mixcr.presets.AlignMixins
 import com.milaboratory.mixcr.presets.AlignMixins.LimitInput
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor.Companion.dotAfterIfNotBlank
 import com.milaboratory.mixcr.presets.FullSampleSheetParsed
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor.Companion.dotAfterIfNotBlank
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.presets.MiXCRParamsSpec
 import com.milaboratory.mixcr.presets.MiXCRStepParams
@@ -127,7 +127,7 @@ import kotlin.io.path.readText
 import kotlin.math.max
 
 object CommandAlign {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.align.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.align.name
 
     const val SAVE_OUTPUT_FILE_NAMES_OPTION = "--save-output-file-names"
     const val STRICT_SAMPLE_NAME_MATCHING_OPTION = "--strict-sample-sheet-matching"
@@ -1165,7 +1165,7 @@ object CommandAlign {
                     MiXCRHeader(
                         inputHash,
                         dontSavePresetOption.presetToSave(paramsSpecPacked),
-                        MiXCRStepParams().add(MiXCRCommandDescriptor.align, cmdParams),
+                        MiXCRStepParams().add(AnalyzeCommandDescriptor.align, cmdParams),
                         tagsExtractor.tagsInfo,
                         aligner.parameters,
                         aligner.parameters.featuresToAlignMap,
@@ -1306,7 +1306,7 @@ object CommandAlign {
                 reportBuilder.setTransformerReports(tagsExtractor.transformerReports)
 
                 val report = reportBuilder.buildReport()
-                writers?.setFooter(MiXCRFooter().addStepReport(MiXCRCommandDescriptor.align, report))
+                writers?.setFooter(MiXCRFooter().addStepReport(AnalyzeCommandDescriptor.align, report))
 
                 // Writing report to stout
                 ReportUtil.writeReportToStdout(report)
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAnalyze.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAnalyze.kt
index 0cb347199..1eea05866 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAnalyze.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAnalyze.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
@@ -22,10 +22,9 @@ import com.milaboratory.mixcr.cli.CommandAlign.inputFileGroups
 import com.milaboratory.mixcr.cli.CommandAlign.listSamplesForSeedFileName
 import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
 import com.milaboratory.mixcr.presets.AlignMixins
-import com.milaboratory.mixcr.presets.AnyMiXCRCommand
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor.Companion.dotAfterIfNotBlank
 import com.milaboratory.mixcr.presets.FullSampleSheetParsed
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor.Companion.dotAfterIfNotBlank
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.presets.MiXCRParamsSpec
 import com.milaboratory.mixcr.presets.MiXCRPipeline
@@ -338,7 +337,7 @@ object CommandAnalyze {
                 .let { (first, second) -> first to second.steps.sortedBy { it.order } }
 
             // Creating execution plan
-            if (pipeline[0] != MiXCRCommandDescriptor.align)
+            if (pipeline[0] != AnalyzeCommandDescriptor.align)
                 throw ValidationException("Pipeline must stat from the align action.")
 
             val planBuilder = PlanBuilder(
@@ -365,7 +364,7 @@ object CommandAnalyze {
             // Adding "align" step
             if (outputNoUsedReads)
                 pathsForNotAligned.fillWithDefaults(inputFileGroups.inputType, outputFolder, outputNamePrefix)
-            planBuilder.addStep(MiXCRCommandDescriptor.align) { _, _, _ ->
+            planBuilder.addStep(AnalyzeCommandDescriptor.align) { _, _, _ ->
                 listOf("--preset", presetName) + extraAlignArgs +
                         mixins.flatMap { it.cmdArgs } + pathsForNotAligned.argsForAlign()
             }
@@ -381,24 +380,24 @@ object CommandAnalyze {
             // Adding all steps with calculations
             pipeline
                 .drop(1)
-                .filter { cmd -> cmd !is MiXCRCommandDescriptor.ExportCommandDescriptor }
+                .filter { cmd -> cmd !is AnalyzeCommandDescriptor.ExportCommandDescriptor }
                 .forEach { cmd ->
                     planBuilder.addStep(cmd) { outputFolder, prefix, sampleName ->
                         when (cmd) {
-                            MiXCRCommandDescriptor.assemble -> {
+                            AnalyzeCommandDescriptor.assemble -> {
                                 val additionalArgs = mutableListOf<String>()
                                 if (consensusAlignments)
                                     additionalArgs += listOf(
                                         "--consensus-alignments",
                                         outputFolder.resolve(
-                                            MiXCRCommandDescriptor.assemble.consensusAlignments(prefix, sampleName)
+                                            AnalyzeCommandDescriptor.assemble.consensusAlignments(prefix, sampleName)
                                         ).toString()
                                     )
                                 if (consensusStateStats)
                                     additionalArgs += listOf(
                                         "--consensus-state-stat",
                                         outputFolder.resolve(
-                                            MiXCRCommandDescriptor.assemble.consensusStateStats(prefix, sampleName)
+                                            AnalyzeCommandDescriptor.assemble.consensusStateStats(prefix, sampleName)
                                         ).toString()
                                     )
                                 consensusStateStatsDownsampling?.let {
@@ -417,7 +416,7 @@ object CommandAnalyze {
             }
 
             pipeline
-                .filterIsInstance<MiXCRCommandDescriptor.ExportCommandDescriptor<*>>()
+                .filterIsInstance<AnalyzeCommandDescriptor.ExportCommandDescriptor<*>>()
                 .forEach { cmd ->
                     planBuilder.addExportStep(cmd)
                 }
@@ -442,9 +441,9 @@ object CommandAnalyze {
             private val forceOverride: Boolean
         ) {
             private val executionPlan = mutableListOf<ExecutionStep>()
-            private val rounds = mutableMapOf<AnyMiXCRCommand, Int>()
+            private val rounds = mutableMapOf<AnalyzeCommandDescriptor<*, *>, Int>()
             private var nextInputs: List<InputFileSet> = listOf(InputFileSet("", initialInputs.map { it.toString() }))
-            private val outputsForCommands = mutableListOf<Pair<AnyMiXCRCommand, List<InputFileSet>>>()
+            private val outputsForCommands = mutableListOf<Pair<AnalyzeCommandDescriptor<*, *>, List<InputFileSet>>>()
 
             fun setActualAlignOutputs(fileNames: List<String>) {
                 val outputSeed = Path(nextInputs.requireSingleton().fileNames.requireSingleton()).name
@@ -483,7 +482,7 @@ object CommandAnalyze {
                 for (input in inputsForQc) {
                     check(input.fileNames.size == 1)
                     val round = 0
-                    val cmd = MiXCRCommandDescriptor.qc
+                    val cmd = AnalyzeCommandDescriptor.qc
                     val outputName = cmd.outputName(outputNamePrefix, input.sampleName, paramsBundle, round)
                     val arguments = mutableListOf("--print-to-stdout")
                     if (forceOverride)
@@ -503,7 +502,7 @@ object CommandAnalyze {
                 }
             }
 
-            fun addExportStep(cmd: MiXCRCommandDescriptor.ExportCommandDescriptor<*>) {
+            fun addExportStep(cmd: AnalyzeCommandDescriptor.ExportCommandDescriptor<*>) {
                 val runAfter = cmd.runAfterLastOf()
                 val inputsForExport = outputsForCommands.findLast { (cmd) -> cmd in runAfter }!!.second
                 for (input in inputsForExport) {
@@ -527,7 +526,7 @@ object CommandAnalyze {
             }
 
             fun addStep(
-                cmd: AnyMiXCRCommand,
+                cmd: AnalyzeCommandDescriptor<*, *>,
                 extraArgs: (outputFolder: Path, prefix: String, sampleName: String) -> List<String> = { _, _, _ -> emptyList() }
             ) {
                 val round = rounds.compute(cmd) { c, p ->
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssemble.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssemble.kt
index b6753f15a..cd4c9cca7 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssemble.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssemble.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
@@ -42,7 +42,7 @@ import com.milaboratory.mixcr.basictypes.tag.TagType
 import com.milaboratory.mixcr.basictypes.validateCompositeFeatures
 import com.milaboratory.mixcr.cli.CommonDescriptions.DEFAULT_VALUE_FROM_PRESET
 import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.util.ArraysUtils
 import com.milaboratory.util.HashFunctions
@@ -66,7 +66,7 @@ import kotlin.io.path.bufferedWriter
 import kotlin.io.path.extension
 
 object CommandAssemble {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.assemble.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.assemble.name
 
     abstract class CmdBase : MiXCRCommandWithOutputs(), MiXCRPresetAwareCommand<CommandAssembleParams> {
         @Option(
@@ -388,7 +388,7 @@ object CommandAssemble {
                     val resultHeader = inputHeader
                         .withAssemblerParameters(cloneAssemblerParameters)
                         .addStepParams(
-                            MiXCRCommandDescriptor.assemble,
+                            AnalyzeCommandDescriptor.assemble,
                             paramsResolver.resolve(paramSpec).second
                         )
                         .copy(paramsSpec = dontSavePresetOption.presetToSave(paramSpec))
@@ -440,7 +440,7 @@ object CommandAssemble {
                             report = reportBuilder.buildReport()
                             writer.setFooter(
                                 alignmentsReader.footer.addStepReport(
-                                    MiXCRCommandDescriptor.assemble,
+                                    AnalyzeCommandDescriptor.assemble,
                                     report
                                 )
                             )
@@ -453,7 +453,7 @@ object CommandAssemble {
                             report = reportBuilder.buildReport()
                             writer.setFooter(
                                 alignmentsReader.footer.addStepReport(
-                                    MiXCRCommandDescriptor.assemble,
+                                    AnalyzeCommandDescriptor.assemble,
                                     report
                                 )
                             )
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssembleContigs.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssembleContigs.kt
index 898925ad2..fbfc7bf43 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssembleContigs.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssembleContigs.kt
@@ -36,7 +36,7 @@ import com.milaboratory.mixcr.basictypes.VDJCSProperties.CloneOrdering
 import com.milaboratory.mixcr.basictypes.validateCompositeFeatures
 import com.milaboratory.mixcr.cli.CommonDescriptions.DEFAULT_VALUE_FROM_PRESET
 import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.presets.MiXCRParamsSpec
 import com.milaboratory.mixcr.util.Concurrency
@@ -66,7 +66,7 @@ import java.nio.file.Path
 import java.util.*
 
 object CommandAssembleContigs {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.assembleContigs.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.assembleContigs.name
 
     abstract class CmdBase : MiXCRCommandWithOutputs(), MiXCRPresetAwareCommand<CommandAssembleContigsParams> {
         @Option(
@@ -172,11 +172,11 @@ object CommandAssembleContigs {
 
                 validateParams(cmdParams, reader.header)
 
-                require(reader.assemblingFeatures.size == 1) {
+                ValidationException.require(reader.assemblingFeatures.size == 1) {
                     "Supports only singular assemblingFeature."
                 }
                 val assemblingFeature = reader.assemblingFeatures.first()
-                require(!assemblingFeature.isComposite) {
+                ValidationException.require(!assemblingFeature.isComposite) {
                     "Supports only non-composite gene features as an assemblingFeature."
                 }
 
@@ -184,7 +184,7 @@ object CommandAssembleContigs {
                     val fullyIncluded = assemblingRegions.features.any { assemblingRegion ->
                         GeneFeature.intersection(assemblingRegion, assemblingFeature) == assemblingFeature
                     }
-                    require(fullyIncluded) {
+                    ValidationException.require(fullyIncluded) {
                         "AssemblingFeature of input must be included fully in assemblingRegions"
                     }
                 }
@@ -305,10 +305,10 @@ object CommandAssembleContigs {
                     clones += clone.withId(cloneId++)
                 }
             }
-            val allFullyCoveredBy = cmdParams.allClonesWillBeCoveredByFeature()
+            val allFullyCoveredBy = cmdParams.parameters.allClonesWillBeCoveredByFeature()
             val resultHeader = header
                 .copy(allFullyCoveredBy = if (allFullyCoveredBy) assemblingRegions else null)
-                .addStepParams(MiXCRCommandDescriptor.assembleContigs, cmdParams)
+                .addStepParams(AnalyzeCommandDescriptor.assembleContigs, cmdParams)
                 .copy(paramsSpec = dontSavePresetOption.presetToSave(paramsSpec))
 
             val cloneSet = CloneSet.Builder(clones, genes, resultHeader)
@@ -327,7 +327,7 @@ object CommandAssembleContigs {
                 // Writing report to stout
                 ReportUtil.writeReportToStdout(report)
                 reportOptions.appendToFiles(report)
-                writer.setFooter(footer.addStepReport(MiXCRCommandDescriptor.assembleContigs, report))
+                writer.setFooter(footer.addStepReport(AnalyzeCommandDescriptor.assembleContigs, report))
             }
         }
     }
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssemblePartial.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssemblePartial.kt
index 1ac831528..7ec8ec70f 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssemblePartial.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssemblePartial.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
@@ -25,7 +25,7 @@ import com.milaboratory.mixcr.basictypes.tag.TagType
 import com.milaboratory.mixcr.cli.CommonDescriptions.DEFAULT_VALUE_FROM_PRESET
 import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
 import com.milaboratory.mixcr.partialassembler.PartialAlignmentsAssembler
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.util.ReportUtil
 import com.milaboratory.util.SmartProgressReporter
@@ -38,7 +38,7 @@ import picocli.CommandLine.Parameters
 import java.nio.file.Path
 
 object CommandAssemblePartial {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.assemblePartial.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.assemblePartial.name
 
     abstract class CmdBase : MiXCRCommandWithOutputs(), MiXCRPresetAwareCommand<CommandAssemblePartialParams> {
         @Option(
@@ -144,7 +144,7 @@ object CommandAssemblePartial {
                 writer.writeHeader(
                     header
                         .updateTagInfo { ti -> ti.setSorted(groupingDepth) } // output data will be grouped only up to a groupingDepth
-                        .addStepParams(MiXCRCommandDescriptor.assemblePartial, cmdParams)
+                        .addStepParams(AnalyzeCommandDescriptor.assemblePartial, cmdParams)
                         .copy(paramsSpec = dontSavePresetOption.presetToSave(paramsSpec)),
                     reader.usedGenes
                 )
@@ -203,7 +203,7 @@ object CommandAssemblePartial {
                 }
                 reportOptions.appendToFiles(report)
                 writer.setNumberOfProcessedReads(reader.numberOfReads - assembler.overlapped.get())
-                writer.setFooter(reader.footer.addStepReport(MiXCRCommandDescriptor.assemblePartial, report))
+                writer.setFooter(reader.footer.addStepReport(AnalyzeCommandDescriptor.assemblePartial, report))
             }
         }
     }
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportAlignments.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportAlignments.kt
index aacccf7ba..eba41db47 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportAlignments.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportAlignments.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
@@ -30,7 +30,7 @@ import com.milaboratory.mixcr.export.InfoWriter
 import com.milaboratory.mixcr.export.MetaForExport
 import com.milaboratory.mixcr.export.RowMetaForExport
 import com.milaboratory.mixcr.export.VDJCAlignmentsFieldsExtractorsFactory
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.util.Concurrency
 import com.milaboratory.util.OutputPortWithProgress
@@ -48,7 +48,7 @@ import picocli.CommandLine.Parameters
 import java.nio.file.Path
 
 object CommandExportAlignments {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.exportAlignments.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.exportAlignments.name
 
     fun CommandExportAlignmentsParams.mkFilter(): Filter<VDJCAlignments> {
         val chainsParsed = Chains.parse(chains)
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportCloneGroups.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportCloneGroups.kt
index 9a32cb92a..b8b9e647d 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportCloneGroups.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportCloneGroups.kt
@@ -32,8 +32,8 @@ import com.milaboratory.mixcr.export.CloneGroupFieldsExtractorsFactory
 import com.milaboratory.mixcr.export.InfoWriter
 import com.milaboratory.mixcr.export.MetaForExport
 import com.milaboratory.mixcr.export.RowMetaForExport
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.ExportMixins
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.util.SubstitutionHelper
 import com.milaboratory.util.asOutputPortWithProgress
@@ -49,7 +49,7 @@ import java.nio.file.Path
 import java.nio.file.Paths
 
 object CommandExportCloneGroups {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.exportCloneGroups.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.exportCloneGroups.name
 
     private fun CommandExportCloneGroupsParams.test(
         clone: Clone,
@@ -116,7 +116,7 @@ object CommandExportCloneGroups {
     }
 
     @Command(
-        description = ["Export clone groups into tab delimited file. Data should be processed by `${MiXCRCommandDescriptor.assembleCells.name}`"]
+        description = ["Export clone groups into tab delimited file. Data should be processed by `${AnalyzeCommandDescriptor.assembleCells.name}`"]
     )
     class Cmd : CmdBase() {
         @Parameters(
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClones.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClones.kt
index 2ba2b51ea..718055802 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClones.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClones.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
@@ -36,7 +36,7 @@ import com.milaboratory.mixcr.export.CloneFieldsExtractorsFactory
 import com.milaboratory.mixcr.export.InfoWriter
 import com.milaboratory.mixcr.export.MetaForExport
 import com.milaboratory.mixcr.export.RowMetaForExport
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.util.SubstitutionHelper
 import com.milaboratory.util.ReportHelper
@@ -55,7 +55,7 @@ import java.nio.file.Path
 import kotlin.io.path.Path
 
 object CommandExportClones {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.exportClones.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.exportClones.name
 
     private fun CommandExportClonesParams.test(
         clone: Clone,
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportPreset.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportPreset.kt
index 716ac150d..7409470cb 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportPreset.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportPreset.kt
@@ -27,7 +27,7 @@ import com.milaboratory.mixcr.basictypes.IOUtil.MiXCRFileType.SHMT
 import com.milaboratory.mixcr.basictypes.IOUtil.MiXCRFileType.VDJCA
 import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader
 import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParams
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.presets.MiXCRParamsSpec
@@ -184,7 +184,7 @@ class CommandExportPreset : MiXCRCommandWithOutputs(), MiXCRPresetAwareCommand<U
                     header.paramsSpec, printParameters = false, validate = false
                 )
 
-                fun <P : MiXCRParams, T : MiXCRCommandDescriptor<P, *>> paramsWithOverride(
+                fun <P : MiXCRParams, T : AnalyzeCommandDescriptor<P, *>> paramsWithOverride(
                     descriptor: T
                 ): P? = header.stepParams[descriptor].firstOrNull() ?: descriptor.extractFromBundle(originalPreset)
 
@@ -192,17 +192,17 @@ class CommandExportPreset : MiXCRCommandWithOutputs(), MiXCRPresetAwareCommand<U
                     flags = originalPreset.flags,
                     pipeline = originalPreset.pipeline,
                     validation = originalPreset.validation,
-                    align = paramsWithOverride(MiXCRCommandDescriptor.align),
-                    refineTagsAndSort = paramsWithOverride(MiXCRCommandDescriptor.refineTagsAndSort),
-                    assemblePartial = paramsWithOverride(MiXCRCommandDescriptor.assemblePartial),
-                    extend = paramsWithOverride(MiXCRCommandDescriptor.extend),
-                    assemble = paramsWithOverride(MiXCRCommandDescriptor.assemble),
-                    assembleContigs = paramsWithOverride(MiXCRCommandDescriptor.assembleContigs),
-                    assembleCells = paramsWithOverride(MiXCRCommandDescriptor.assembleCells),
-                    exportAlignments = paramsWithOverride(MiXCRCommandDescriptor.exportAlignments),
-                    exportClones = paramsWithOverride(MiXCRCommandDescriptor.exportClones),
-                    exportCloneGroups = paramsWithOverride(MiXCRCommandDescriptor.exportCloneGroups),
-                    qc = paramsWithOverride(MiXCRCommandDescriptor.qc)
+                    align = paramsWithOverride(AnalyzeCommandDescriptor.align),
+                    refineTagsAndSort = paramsWithOverride(AnalyzeCommandDescriptor.refineTagsAndSort),
+                    assemblePartial = paramsWithOverride(AnalyzeCommandDescriptor.assemblePartial),
+                    extend = paramsWithOverride(AnalyzeCommandDescriptor.extend),
+                    assemble = paramsWithOverride(AnalyzeCommandDescriptor.assemble),
+                    assembleContigs = paramsWithOverride(AnalyzeCommandDescriptor.assembleContigs),
+                    assembleCells = paramsWithOverride(AnalyzeCommandDescriptor.assembleCells),
+                    exportAlignments = paramsWithOverride(AnalyzeCommandDescriptor.exportAlignments),
+                    exportClones = paramsWithOverride(AnalyzeCommandDescriptor.exportClones),
+                    exportCloneGroups = paramsWithOverride(AnalyzeCommandDescriptor.exportCloneGroups),
+                    qc = paramsWithOverride(AnalyzeCommandDescriptor.qc)
                 )
                 ParamsBundleSpecBaseEmbedded(bundle)
             }
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportReports.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportReports.kt
index a263a4d10..5d6594311 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportReports.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportReports.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportReportsAsTable.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportReportsAsTable.kt
index 118635ae7..00527f9b0 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportReportsAsTable.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportReportsAsTable.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportSchemas.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportSchemas.kt
index 41c171f5c..fc8637226 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportSchemas.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportSchemas.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
@@ -25,7 +25,7 @@ import com.milaboratory.mixcr.assembler.preclone.PreCloneAssemblerParameters
 import com.milaboratory.mixcr.partialassembler.PartialAlignmentsAssemblerParameters
 import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersIndividual
 import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersOverlap
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRMixin
 import com.milaboratory.mixcr.trees.CommandFindShmTreesParams
 import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters
@@ -112,7 +112,7 @@ class CommandExportSchemas : Runnable {
         val analyzeBundleDir = outputPath.resolve("analyzeBundle")
         val parametersDir = analyzeBundleDir.resolve("parameters")
         parametersDir.toFile().mkdirs()
-        for (command in MiXCRCommandDescriptor::class.sealedFinalSubclasses()) {
+        for (command in AnalyzeCommandDescriptor::class.sealedFinalSubclasses()) {
             val parameters = command.objectInstance?.paramClass!!
             K_YAML_OM.writeValue(
                 parametersDir.resolve("${command.simpleName}.schema.yaml").toFile(),
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExtend.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExtend.kt
index 427558620..b7bcf9c38 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExtend.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExtend.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
@@ -33,7 +33,7 @@ import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter
 import com.milaboratory.mixcr.basictypes.VDJCObject
 import com.milaboratory.mixcr.cli.CommonDescriptions.DEFAULT_VALUE_FROM_PRESET
 import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.presets.MiXCRParamsSpec
 import com.milaboratory.mixcr.util.VDJCObjectExtender
@@ -53,7 +53,7 @@ import java.nio.file.Path
 
 
 object CommandExtend {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.extend.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.extend.name
 
     abstract class CmdBase : MiXCRCommandWithOutputs(), MiXCRPresetAwareCommand<CommandExtendParams> {
         @Option(
@@ -185,7 +185,7 @@ object CommandExtend {
                     process.output.toList(),
                     cloneSet.usedGenes,
                     cloneSet.header
-                        .addStepParams(MiXCRCommandDescriptor.extend, process.params)
+                        .addStepParams(AnalyzeCommandDescriptor.extend, process.params)
                         .copy(allFullyCoveredBy = null)
                         .copy(paramsSpec = dontSavePresetOption.presetToSave(paramsSpec))
                 )
@@ -195,7 +195,7 @@ object CommandExtend {
                 ClnsWriter(outputFile).use { writer ->
                     writer.writeCloneSet(newCloneSet)
                     val report = process.finish()
-                    writer.setFooter(reader.footer.addStepReport(MiXCRCommandDescriptor.extend, report))
+                    writer.setFooter(reader.footer.addStepReport(AnalyzeCommandDescriptor.extend, report))
                 }
             }
         }
@@ -209,7 +209,7 @@ object CommandExtend {
                     writer.writeHeader(
                         reader.header
                             .copy(paramsSpec = dontSavePresetOption.presetToSave(paramsSpec))
-                            .addStepParams(MiXCRCommandDescriptor.extend, process.params),
+                            .addStepParams(AnalyzeCommandDescriptor.extend, process.params),
                         reader.usedGenes
                     )
                     writer.setFooter(reader.footer)
@@ -226,7 +226,7 @@ object CommandExtend {
 
                     writer.setNumberOfProcessedReads(reader.numberOfReads)
                     val report = process.finish()
-                    writer.setFooter(reader.footer.addStepReport(MiXCRCommandDescriptor.extend, report))
+                    writer.setFooter(reader.footer.addStepReport(AnalyzeCommandDescriptor.extend, report))
                 }
             }
         }
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindAlleles.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindAlleles.kt
index 4b161ccaf..f9019b3dc 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindAlleles.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindAlleles.kt
@@ -75,12 +75,10 @@ import picocli.CommandLine.Option
 import picocli.CommandLine.Parameters
 import java.io.File
 import java.nio.file.Path
-import java.nio.file.Paths
 import kotlin.collections.set
 import kotlin.io.path.createDirectories
 import kotlin.io.path.isDirectory
 import kotlin.io.path.listDirectoryEntries
-import kotlin.io.path.nameWithoutExtension
 
 @Command(
     description = [
@@ -110,12 +108,7 @@ class CommandFindAlleles : MiXCRCommandWithOutputs() {
 
     class OutputClnsOptions {
         @Option(
-            description = [
-                "Output template may contain {file_name} and {file_dir_path},",
-                "outputs for '-o /output/folder/{file_name}_with_alleles.clns input_file.clns input_file2.clns' will be /output/folder/input_file_with_alleles.clns and /output/folder/input_file2_with_alleles.clns,",
-                "outputs for '-o {file_dir_path}/{file_name}_with_alleles.clns /some/folder1/input_file.clns /some/folder2/input_file2.clns' will be /seme/folder1/input_file_with_alleles.clns and /some/folder2/input_file2_with_alleles.clns",
-                "Resulted outputs must be uniq"
-            ],
+            description = [OutputTemplate.description],
             names = ["--output-template"],
             paramLabel = "<template.clns>",
             required = true,
@@ -200,7 +193,7 @@ class CommandFindAlleles : MiXCRCommandWithOutputs() {
 
     @Option(
         names = ["-O"],
-        description = ["Overrides default build SHM parameter values"],
+        description = ["Overrides default find alleles parameter values"],
         paramLabel = Labels.OVERRIDES,
         order = OptionsOrder.overrides
     )
@@ -215,24 +208,7 @@ class CommandFindAlleles : MiXCRCommandWithOutputs() {
 
     private val outputClnsFiles: List<Path> by lazy {
         val template = outputClnsOptions.outputTemplate ?: return@lazy emptyList()
-        if (!template.endsWith(".clns")) {
-            throw ValidationException("Wrong template: command produces only clns, got $template")
-        }
-        val clnsFiles = inputFiles
-            .map { it.toAbsolutePath() }
-            .map { path ->
-                template
-                    .replace(Regex("\\{file_name}"), path.nameWithoutExtension)
-                    .replace(Regex("\\{file_dir_path}"), path.parent.toString())
-            }
-            .map { Paths.get(it) }
-            .toList()
-        if (clnsFiles.distinct().count() < clnsFiles.size) {
-            var message = "Output clns files are not uniq: $clnsFiles"
-            message += "\nTry to use `{file_name}` and/or `{file_dir_path}` in template to get different output paths for every input. See help for more details"
-            throw ValidationException(message)
-        }
-        clnsFiles
+        OutputTemplate.calculateOutputs(template, inputFiles)
     }
 
     public override val outputFiles get() = outputClnsFiles + listOfNotNull(allelesMutationsOutput) + libraryOutputs
@@ -262,6 +238,12 @@ class CommandFindAlleles : MiXCRCommandWithOutputs() {
         libraryOutputs.forEach { output ->
             ValidationException.requireFileType(output, InputFileType.JSON, InputFileType.FASTA)
         }
+        outputClnsOptions.outputTemplate?.let { template ->
+            if (!template.endsWith(".clns")) {
+                throw ValidationException("Wrong template: command produces only clns, got $template")
+            }
+        }
+
         if ((listOfNotNull(outputClnsOptions.outputTemplate, allelesMutationsOutput) + libraryOutputs).isEmpty()) {
             throw ValidationException("--output-template, --export-library or --export-alleles-mutations must be set")
         }
@@ -345,8 +327,7 @@ class CommandFindAlleles : MiXCRCommandWithOutputs() {
         val baseGenes = originalLibrary.allGenes
             .mapNotNull { it.data.alleleInfo?.parent }
             .distinct()
-        val absentBaseGenes = baseGenes.filter { it !in originalLibrary }
-        ValidationException.requireEmpty(absentBaseGenes) {
+        ValidationException.requireEmpty(baseGenes.filter { it !in originalLibrary }) {
             "All base genes must be presented in the library"
         }
 
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindShmTrees.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindShmTrees.kt
index 512544ed5..1044fdd05 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindShmTrees.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindShmTrees.kt
@@ -33,6 +33,7 @@ import com.milaboratory.mixcr.basictypes.tag.TagType
 import com.milaboratory.mixcr.basictypes.tag.TagsInfo
 import com.milaboratory.mixcr.basictypes.validateCompositeFeatures
 import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.AssembleContigsMixins
 import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsSpec
@@ -411,7 +412,7 @@ class CommandFindShmTrees : MiXCRCommandWithOutputs() {
                 val filesToGroup = inputFiles
                     .filterIndexed { index, _ -> index in datasetsThatShouldHaveGroups }
                     .joinToString(", ")
-                "Can't use information about cell, run `${MiXCRCommandDescriptor.assembleCells}` for $filesToGroup"
+                "Can't use information about cell, run `${AnalyzeCommandDescriptor.assembleCells}` for $filesToGroup"
             }
         }
         return datasetsWithGroups
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandGroupClones.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandGroupClones.kt
index 8c8bff905..202df6867 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandGroupClones.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandGroupClones.kt
@@ -30,7 +30,7 @@ import com.milaboratory.mixcr.basictypes.MiXCRHeader
 import com.milaboratory.mixcr.basictypes.VDJCAlignments
 import com.milaboratory.mixcr.basictypes.tag.TagType
 import com.milaboratory.mixcr.clonegrouping.CloneGroupingParams.Companion.mkGrouper
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.util.Concurrency
 import com.milaboratory.util.ReportUtil
@@ -44,7 +44,7 @@ import picocli.CommandLine.Parameters
 import java.nio.file.Path
 
 object CommandGroupClones {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.assembleCells.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.assembleCells.name
 
     abstract class CmdBase : MiXCRCommandWithOutputs(), MiXCRPresetAwareCommand<CommandGroupClonesParams> {
         @Option(
@@ -129,7 +129,7 @@ object CommandGroupClones {
                     writer.writeCloneSet(result)
                     reportBuilder.setFinishMillis(System.currentTimeMillis())
                     val report = reportBuilder.buildReport()
-                    writer.setFooter(reader.footer.addStepReport(MiXCRCommandDescriptor.assembleCells, report))
+                    writer.setFooter(reader.footer.addStepReport(AnalyzeCommandDescriptor.assembleCells, report))
                     report
                 }
             }
@@ -154,7 +154,7 @@ object CommandGroupClones {
                     writer.collateAlignments(allAlignmentsList.flatten(), newNumberOfAlignments)
                     reportBuilder.setFinishMillis(System.currentTimeMillis())
                     val report = reportBuilder.buildReport()
-                    writer.setFooter(reader.footer.addStepReport(MiXCRCommandDescriptor.assembleCells, report))
+                    writer.setFooter(reader.footer.addStepReport(AnalyzeCommandDescriptor.assembleCells, report))
                     writer.writeAlignmentsAndIndex()
                     report
                 }
@@ -195,7 +195,7 @@ object CommandGroupClones {
                 input.usedGenes,
                 input.header
                     .copy(calculatedCloneGroups = true)
-                    .addStepParams(MiXCRCommandDescriptor.assembleCells, cmdParams)
+                    .addStepParams(AnalyzeCommandDescriptor.assembleCells, cmdParams)
                     .copy(paramsSpec = dontSavePresetOption.presetToSave(paramsSpec))
             )
                 .sort(input.ordering)
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandQcChecks.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandQcChecks.kt
index 1e8198b47..4f6ef2c18 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandQcChecks.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandQcChecks.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
@@ -19,7 +19,7 @@ import com.milaboratory.cli.POverridesBuilderOps
 import com.milaboratory.cli.ParamsResolver
 import com.milaboratory.mixcr.basictypes.IOUtil
 import com.milaboratory.mixcr.cli.MiXCRMixinCollection.Companion.mixins
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.qc.checks.QcCheckResult
 import com.milaboratory.mixcr.qc.checks.QcChecker.QualityStatus.ALERT
@@ -36,7 +36,7 @@ import java.io.PrintStream
 import java.nio.file.Path
 
 object CommandQcChecks {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.qc.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.qc.name
 
     abstract class CmdBase : MiXCRCommandWithOutputs(), MiXCRPresetAwareCommand<CommandQcChecksParams> {
         @Mixin
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandRefineTagsAndSort.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandRefineTagsAndSort.kt
index 4f2d3b0a7..e708dc8aa 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandRefineTagsAndSort.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandRefineTagsAndSort.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
@@ -39,7 +39,7 @@ import com.milaboratory.mixcr.basictypes.tag.TagValueType
 import com.milaboratory.mixcr.basictypes.tag.tagAliases
 import com.milaboratory.mixcr.cli.CommonDescriptions.DEFAULT_VALUE_FROM_PRESET
 import com.milaboratory.mixcr.cli.MiXCRMixinCollection.Companion.mixins
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.presets.RefineTagsAndSortMixins
 import com.milaboratory.mixcr.util.MiXCRVersionInfo
@@ -61,7 +61,7 @@ import java.nio.file.Path
 import java.util.*
 
 object CommandRefineTagsAndSort {
-    const val COMMAND_NAME = MiXCRCommandDescriptor.refineTagsAndSort.name
+    const val COMMAND_NAME = AnalyzeCommandDescriptor.refineTagsAndSort.name
 
     abstract class CmdBase : MiXCRCommandWithOutputs(), MiXCRPresetAwareCommand<CommandRefineTagsAndSortParams> {
         @Option(
@@ -436,7 +436,7 @@ object CommandRefineTagsAndSort {
                     writer.writeHeader(
                         header
                             .updateTagInfo { tagsInfo -> tagsInfo.setSorted(tagsInfo.size) }
-                            .addStepParams(MiXCRCommandDescriptor.refineTagsAndSort, cmdParams)
+                            .addStepParams(AnalyzeCommandDescriptor.refineTagsAndSort, cmdParams)
                             .copy(paramsSpec = dontSavePresetOption.presetToSave(paramsSpec)),
                         mainReader.usedGenes
                     )
@@ -454,7 +454,7 @@ object CommandRefineTagsAndSort {
                     writer.setFooter(
                         mainReader.footer
                             .withThresholds(thresholds)
-                            .addStepReport(MiXCRCommandDescriptor.refineTagsAndSort, refineTagsAndSortReport)
+                            .addStepReport(AnalyzeCommandDescriptor.refineTagsAndSort, refineTagsAndSortReport)
                     )
                 }
             }
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/MiXCRParamsResolver.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/MiXCRParamsResolver.kt
index f00c0f8c6..84f408345 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/MiXCRParamsResolver.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/MiXCRParamsResolver.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
@@ -17,8 +17,8 @@ import com.milaboratory.cli.PresetAware
 import com.milaboratory.mixcr.basictypes.HasFeatureToAlign
 import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
 import com.milaboratory.mixcr.presets.AlignMixins
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.Flags
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRMixin
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.presets.Presets
@@ -39,18 +39,18 @@ abstract class MiXCRParamsResolver<P : Any>(
             throw ValidationException("Error validating preset bundle.");
         }
         if (
-            bundle.pipeline?.steps?.contains(MiXCRCommandDescriptor.assembleContigs) == true &&
+            bundle.pipeline?.steps?.contains(AnalyzeCommandDescriptor.assembleContigs) == true &&
             bundle.assemble?.clnaOutput == false
         )
             throw ValidationException("assembleContigs step required clnaOutput=true on assemble step")
 
         bundle.align?.parameters?.featuresToAlignMap?.let { HasFeatureToAlign(it) }?.let { featuresToAlign ->
-            if (bundle.pipeline?.steps?.contains(MiXCRCommandDescriptor.assemble) == true) {
+            if (bundle.pipeline?.steps?.contains(AnalyzeCommandDescriptor.assemble) == true) {
                 bundle.assemble?.let { params ->
                     CommandAssemble.validateParams(params, featuresToAlign)
                 }
             }
-            if (bundle.pipeline?.steps?.contains(MiXCRCommandDescriptor.assembleContigs) == true) {
+            if (bundle.pipeline?.steps?.contains(AnalyzeCommandDescriptor.assembleContigs) == true) {
                 bundle.assembleContigs?.let { params ->
                     CommandAssembleContigs.validateParams(params, featuresToAlign)
                 }
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/Mixins.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/Mixins.kt
index 3141107a8..b2eb64075 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/Mixins.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/Mixins.kt
@@ -33,6 +33,7 @@ import com.milaboratory.mixcr.presets.AlignMixins.RightAlignmentBoundaryWithPoin
 import com.milaboratory.mixcr.presets.AlignMixins.SetLibrary
 import com.milaboratory.mixcr.presets.AlignMixins.SetSpecies
 import com.milaboratory.mixcr.presets.AlignMixins.SetTagPattern
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.AssembleContigsMixins.SetContigAssemblingFeatures
 import com.milaboratory.mixcr.presets.AssembleMixins.SetClonotypeAssemblingFeatures
 import com.milaboratory.mixcr.presets.AssembleMixins.SetSplitClonesBy
@@ -43,7 +44,6 @@ import com.milaboratory.mixcr.presets.ExportMixins.AddExportClonesField
 import com.milaboratory.mixcr.presets.ExportMixins.DontImputeGermlineOnExport
 import com.milaboratory.mixcr.presets.ExportMixins.ImputeGermlineOnExport
 import com.milaboratory.mixcr.presets.GenericMixin
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
 import com.milaboratory.mixcr.presets.PipelineMixins.AddPipelineStep
 import com.milaboratory.mixcr.presets.PipelineMixins.RemovePipelineStep
 import com.milaboratory.mixcr.presets.QcMixins
@@ -699,9 +699,9 @@ object ExportMiXCRMixins {
         @Option(
             description = [
                 "Filter out clones from groups of particular type.",
-                "`found` - groups that were found on `${MiXCRCommandDescriptor.assembleCells.name}`.",
-                "`undefined` - there were not enough info on `${MiXCRCommandDescriptor.assembleCells.name}` to form a group.",
-                "`contamination` - clones that were marked as contamination on `${MiXCRCommandDescriptor.assembleCells.name}`.",
+                "`found` - groups that were found on `${AnalyzeCommandDescriptor.assembleCells.name}`.",
+                "`undefined` - there were not enough info on `${AnalyzeCommandDescriptor.assembleCells.name}` to form a group.",
+                "`contamination` - clones that were marked as contamination on `${AnalyzeCommandDescriptor.assembleCells.name}`.",
             ],
             names = [ExportMixins.FilterOutCloneGroupTypes.CMD_OPTION],
             arity = "1..*",
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/OutputTemplate.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/OutputTemplate.kt
new file mode 100644
index 000000000..0231cbdd0
--- /dev/null
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/OutputTemplate.kt
@@ -0,0 +1,42 @@
+/*
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
+ *
+ * Before downloading or accessing the software, please read carefully the
+ * License Agreement available at:
+ * https://github.com/milaboratory/mixcr/blob/develop/LICENSE
+ *
+ * By downloading or accessing the software, you accept and agree to be bound
+ * by the terms of the License Agreement. If you do not want to agree to the terms
+ * of the Licensing Agreement, you must not download or access the software.
+ */
+package com.milaboratory.mixcr.cli
+
+import com.milaboratory.app.ValidationException
+import java.nio.file.Path
+import java.nio.file.Paths
+import kotlin.io.path.nameWithoutExtension
+
+object OutputTemplate {
+    const val description = "Output template may contain {file_name} and {file_dir_path},%n" +
+            "outputs for '-o /output/folder/{file_name}_suffix.clns input_file.clns input_file2.clns' will be /output/folder/input_file_suffix.clns and /output/folder/input_file2_suffix.clns,%n" +
+            "outputs for '-o {file_dir_path}/{file_name}_suffix.clns /some/folder1/input_file.clns /some/folder2/input_file2.clns' will be /seme/folder1/input_file_suffix.clns and /some/folder2/input_file2_suffix.clns%n" +
+            "Resulted outputs must be uniq"
+
+    fun calculateOutputs(template: String, inputFiles: List<Path>): List<Path> {
+        val outputFiles = inputFiles
+            .map { it.toAbsolutePath() }
+            .map { path ->
+                template
+                    .replace(Regex("\\{file_name}"), path.nameWithoutExtension)
+                    .replace(Regex("\\{file_dir_path}"), path.parent.toString())
+            }
+            .map { Paths.get(it) }
+            .toList()
+        if (outputFiles.distinct().count() < outputFiles.size) {
+            var message = "Output files are not uniq: $outputFiles"
+            message += "\nTry to use `{file_name}` and/or `{file_dir_path}` in template to get different output paths for every input. See help for more details"
+            throw ValidationException(message)
+        }
+        return outputFiles
+    }
+}
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/qc/CommandExportQcTags.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/qc/CommandExportQcTags.kt
index a260e802d..0d4c271e5 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/qc/CommandExportQcTags.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/qc/CommandExportQcTags.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
@@ -21,7 +21,7 @@ import com.milaboratory.mixcr.cli.CommandRefineTagsAndSort
 import com.milaboratory.mixcr.cli.CommonDescriptions.Labels
 import com.milaboratory.mixcr.cli.MiXCRCommandWithOutputs
 import com.milaboratory.mixcr.cli.exportTypes
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.qc.plots.TagRefinementQc
 import picocli.CommandLine
 import picocli.CommandLine.Command
@@ -101,7 +101,7 @@ class CommandExportQcTags : MiXCRCommandWithOutputs() {
     override fun run1() {
         val plots = inputFiles.mapNotNull { file ->
             val info = IOUtil.extractFileInfo(file)
-            val report = info.footer.reports[MiXCRCommandDescriptor.refineTagsAndSort]
+            val report = info.footer.reports[AnalyzeCommandDescriptor.refineTagsAndSort]
             if (report.isEmpty()) {
                 println("No tag refinement report for $file; did you run ${CommandRefineTagsAndSort.COMMAND_NAME} command?")
                 null
diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java
index b862bf636..be8121814 100644
--- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java
+++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved
+ * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved
  *
  * Before downloading or accessing the software, please read carefully the
  * License Agreement available at:
@@ -53,4 +53,4 @@ public void test1() throws Exception {
         VDJCAlignerParameters clone = deser.clone();
         assertEquals(paramentrs, clone);
     }
-}
\ No newline at end of file
+}
diff --git a/src/test/kotlin/com/milaboratory/mixcr/PresetsTest.kt b/src/test/kotlin/com/milaboratory/mixcr/PresetsTest.kt
index 874229477..07660e233 100644
--- a/src/test/kotlin/com/milaboratory/mixcr/PresetsTest.kt
+++ b/src/test/kotlin/com/milaboratory/mixcr/PresetsTest.kt
@@ -11,7 +11,7 @@ import com.milaboratory.mixcr.cli.presetFlagsMessages
 import com.milaboratory.mixcr.export.CloneFieldsExtractorsFactory
 import com.milaboratory.mixcr.export.MetaForExport
 import com.milaboratory.mixcr.export.VDJCAlignmentsFieldsExtractorsFactory
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.mixcr.presets.MiXCRPresetCategory
 import com.milaboratory.mixcr.presets.Presets
@@ -152,7 +152,7 @@ class PresetsTest {
     fun `all presets should have exportClones step`() {
         Presets.nonAbstractPresetNames.filter { presetName ->
             val bundle = Presets.MiXCRBundleResolver.resolvePreset(presetName)
-            MiXCRCommandDescriptor.exportClones !in bundle.pipeline!!.steps
+            AnalyzeCommandDescriptor.exportClones !in bundle.pipeline!!.steps
         } shouldBe emptyList()
     }
 
@@ -162,7 +162,7 @@ class PresetsTest {
             presetName.asClue {
                 val bundle = Presets.MiXCRBundleResolver.resolvePreset(presetName)
                 bundle.pipeline!!.steps
-                    .filterIsInstance<MiXCRCommandDescriptor.ExportCommandDescriptor<*>>()
+                    .filterIsInstance<AnalyzeCommandDescriptor.ExportCommandDescriptor<*>>()
                     .forEach { exportStep ->
                         exportStep.command.asClue {
                             bundle.pipeline!!.steps shouldContainAnyOf exportStep.runAfterLastOf()
@@ -177,11 +177,11 @@ class PresetsTest {
         Presets.nonAbstractPresetNames
             .filter { presetName ->
                 val bundle = Presets.MiXCRBundleResolver.resolvePreset(presetName)
-                MiXCRCommandDescriptor.assembleCells in bundle.pipeline!!.steps
+                AnalyzeCommandDescriptor.assembleCells in bundle.pipeline!!.steps
             }
             .filter { presetName ->
                 val bundle = Presets.MiXCRBundleResolver.resolvePreset(presetName)
-                MiXCRCommandDescriptor.exportCloneGroups !in bundle.pipeline!!.steps
+                AnalyzeCommandDescriptor.exportCloneGroups !in bundle.pipeline!!.steps
             } shouldBe emptyList()
     }
 
diff --git a/src/test/kotlin/com/milaboratory/mixcr/cli/CommandExportPresetTest.kt b/src/test/kotlin/com/milaboratory/mixcr/cli/CommandExportPresetTest.kt
index f689c2673..139dfb81b 100644
--- a/src/test/kotlin/com/milaboratory/mixcr/cli/CommandExportPresetTest.kt
+++ b/src/test/kotlin/com/milaboratory/mixcr/cli/CommandExportPresetTest.kt
@@ -2,7 +2,7 @@ package com.milaboratory.mixcr.cli
 
 import com.fasterxml.jackson.module.kotlin.readValue
 import com.milaboratory.mixcr.export.ExportFieldDescription
-import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRParamsBundle
 import com.milaboratory.util.K_YAML_OM
 import com.milaboratory.util.TempFileManager
@@ -52,7 +52,7 @@ class CommandExportPresetTest {
         output.delete()
         TestMain.execute("exportPreset --species hs --floating-left-alignment-boundary --floating-right-alignment-boundary C --dna --add-step assembleContigs --preset-name test-tcr-shotgun ${output.path}")
         val result = K_YAML_OM.readValue<MiXCRParamsBundle>(output)
-        result.pipeline!!.steps shouldContain MiXCRCommandDescriptor.assembleContigs
+        result.pipeline!!.steps shouldContain AnalyzeCommandDescriptor.assembleContigs
         result.assemble!!.clnaOutput shouldBe true
     }
 
@@ -62,8 +62,8 @@ class CommandExportPresetTest {
         output.delete()
         TestMain.execute("exportPreset --floating-left-alignment-boundary --floating-right-alignment-boundary C --species hs --dna --remove-step exportClones --remove-step exportAlignments --preset-name test-tcr-shotgun ${output.path}")
         val result = K_YAML_OM.readValue<MiXCRParamsBundle>(output)
-        result.pipeline!!.steps shouldNotContain MiXCRCommandDescriptor.exportClones
-        result.pipeline!!.steps shouldNotContain MiXCRCommandDescriptor.exportAlignments
+        result.pipeline!!.steps shouldNotContain AnalyzeCommandDescriptor.exportClones
+        result.pipeline!!.steps shouldNotContain AnalyzeCommandDescriptor.exportAlignments
     }
 
     @Test
@@ -85,8 +85,8 @@ class CommandExportPresetTest {
         val result = K_YAML_OM.readValue<MiXCRParamsBundle>(output)
         result.flags shouldBe emptySet()
         result.align!!.species shouldBe "hsa"
-        result.pipeline!!.steps shouldNotContain MiXCRCommandDescriptor.exportClones
-        result.pipeline!!.steps shouldNotContain MiXCRCommandDescriptor.exportAlignments
+        result.pipeline!!.steps shouldNotContain AnalyzeCommandDescriptor.exportClones
+        result.pipeline!!.steps shouldNotContain AnalyzeCommandDescriptor.exportAlignments
         result.align!!.tagPattern shouldBe "^(R1F:N{0:2}(C:gggggaaaagggttg)(R1:*))"
         result.align!!.tagUnstranded shouldBe true
         result.align!!.limit shouldBe 1000
diff --git a/src/test/kotlin/com/milaboratory/mixcr/cli/CommandFindAllelesTest.kt b/src/test/kotlin/com/milaboratory/mixcr/cli/CommandFindAllelesTest.kt
index 9cc85f4d4..5a893af6b 100644
--- a/src/test/kotlin/com/milaboratory/mixcr/cli/CommandFindAllelesTest.kt
+++ b/src/test/kotlin/com/milaboratory/mixcr/cli/CommandFindAllelesTest.kt
@@ -15,11 +15,11 @@ import com.milaboratory.app.ValidationException
 import com.milaboratory.util.TempFileDest
 import com.milaboratory.util.TempFileManager
 import io.kotest.matchers.collections.shouldContainExactlyInAnyOrder
+import io.kotest.matchers.string.shouldStartWith
 import org.junit.Assert
 import org.junit.Before
 import org.junit.Test
 import picocli.CommandLine
-import java.io.IOException
 import java.nio.file.Path
 import java.nio.file.Paths
 
@@ -30,7 +30,6 @@ class CommandFindAllelesTest {
     private val file3: Path = temp.resolvePath("folder3/file1.clns")
 
     @Before
-    @Throws(IOException::class)
     fun prepareFiles() {
         file1.toFile().parentFile.mkdirs()
         file1.toFile().createNewFile()
@@ -122,7 +121,7 @@ class CommandFindAllelesTest {
             command.outputFiles
             Assert.fail()
         } catch (e: ValidationException) {
-            Assert.assertTrue(e.message, e.message.startsWith("Output clns files are not uniq:"))
+            e.message shouldStartWith "Output files are not uniq:"
         }
     }
 
@@ -136,7 +135,7 @@ class CommandFindAllelesTest {
         ).parseResult
         val command = p.asCommandLineList()[p.asCommandLineList().size - 1].getCommand<CommandFindAlleles>()
         try {
-            command.outputFiles
+            command.validate()
             Assert.fail()
         } catch (e: ValidationException) {
             Assert.assertEquals(
diff --git a/src/test/kotlin/com/milaboratory/mixcr/cli/MetaInfoTest.kt b/src/test/kotlin/com/milaboratory/mixcr/cli/MetaInfoTest.kt
index a5fd5f709..2501c18f1 100644
--- a/src/test/kotlin/com/milaboratory/mixcr/cli/MetaInfoTest.kt
+++ b/src/test/kotlin/com/milaboratory/mixcr/cli/MetaInfoTest.kt
@@ -1,5 +1,6 @@
 package com.milaboratory.mixcr.cli
 
+import com.milaboratory.mixcr.presets.AnalyzeCommandDescriptor
 import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor
 import io.kotest.assertions.withClue
 import io.kotest.matchers.shouldBe
@@ -13,7 +14,7 @@ class MetaInfoTest {
         mixcrCommandDescriptions()
             .map { it.command }
             .filter { commandName ->
-                MiXCRCommandDescriptor.fromStringOrNull(commandName) == null
+                AnalyzeCommandDescriptor.fromStringOrNull(commandName) == null
             } shouldBe emptyList()
     }
 
@@ -24,7 +25,7 @@ class MetaInfoTest {
             MiXCRCommandDescriptor.findAlleles,
             MiXCRCommandDescriptor.findShmTrees,
 
-            MiXCRCommandDescriptor.align
+            AnalyzeCommandDescriptor.align
         )
         (mixcrCommandDescriptions() - exclusions)
             .map { it.command }
@@ -41,10 +42,10 @@ class MetaInfoTest {
             MiXCRCommandDescriptor.findAlleles,
             MiXCRCommandDescriptor.findShmTrees,
 
-            MiXCRCommandDescriptor.exportClones,
-            MiXCRCommandDescriptor.exportCloneGroups,
-            MiXCRCommandDescriptor.exportAlignments,
-            MiXCRCommandDescriptor.qc,
+            AnalyzeCommandDescriptor.exportClones,
+            AnalyzeCommandDescriptor.exportCloneGroups,
+            AnalyzeCommandDescriptor.exportAlignments,
+            AnalyzeCommandDescriptor.qc,
         )
         (mixcrCommandDescriptions() - exclusions)
             .map { it.command }
@@ -55,7 +56,7 @@ class MetaInfoTest {
     }
 
     private fun mixcrCommandDescriptions() =
-        MiXCRCommandDescriptor::class.resolveSealedSubclasses().map { it.objectInstance!! }
+        AnalyzeCommandDescriptor::class.resolveSealedSubclasses().map { it.objectInstance!! }
 
     private fun <T : Any> KClass<T>.resolveSealedSubclasses(): List<KClass<out T>> =
         when {