diff --git a/build.gradle.kts b/build.gradle.kts
index 78f355074..0c2245ec1 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 = "4.7.0-31-fixes"
+val mixcrAlgoVersion = "4.7.0-35-exports-for-trees"
 // 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/changelogs/v4.7.1.md b/changelogs/v4.7.1.md
index b5f05ad9b..9577a8a96 100644
--- a/changelogs/v4.7.1.md
+++ b/changelogs/v4.7.1.md
@@ -1,9 +1,19 @@
+## ❗ Breaking changes
+
+- Shortcut options `-p` and `-pf` are removed from export commands. They are conflicting with new added export fields
+  `-pN`, `-pS` and `-pNpS`
+
 ## 🛠️ Other improvements & fixes
 
 - Tracking the progres of fasta[.gz] inputs on `align`.
 - Improved alignment rate of short parts of genes in reads with height rate of mutations
 - Fixed combination of `-Massemble.sortBySequence=true` and `--assemble-clonotypes-by` with composite feature
 - For `findShmTree` command `--alleles-search-could-be-skipped` option is added for special cases
+- Added `[withAlignmentGaps]` option to features exports in `exportShmTreesWithNodes` command. That will add gaps, so
+  results could be interpreted as alignments of all nodes to root sequence
+- Added `-pN`, `-pS`, `-pNpS` options for `exportShmTreesWithNodes` command
+- Fixed `findShmTrees` command. Now it outputs root node with the reconstructed NDN region (before it was filled with N
+  letters)
 
 ## 📚 New Presets
 
diff --git a/regression/cli-help/exportReportsTable.txt b/regression/cli-help/exportReportsTable.txt
index d4afb0237..564351fd9 100644
--- a/regression/cli-help/exportReportsTable.txt
+++ b/regression/cli-help/exportReportsTable.txt
@@ -32,8 +32,8 @@ Export reports from files in tabular format.
       [report.tsv]           Path where to write reports. Print in stdout if omitted.
       --without-upstreams    Don't export upstream reports for sources of steps with several
                                inputs, like `findShmTrees`.
-  -p, --preset <preset>      Specify preset of export fields. Possible values: min, full.
-      -pf, --preset-file <presetFile>
+      --preset <preset>      Specify preset of export fields. Possible values: min, full.
+      --preset-file <presetFile>
                              Specify preset file of export fields
       --no-header            Don't print first header line, print only data
   -f, --force-overwrite      Force overwrite of output file(s).
diff --git a/regression/cli-help/exportShmSingleCellTrees.txt b/regression/cli-help/exportShmSingleCellTrees.txt
index f36859b8b..390b4466a 100644
--- a/regression/cli-help/exportShmSingleCellTrees.txt
+++ b/regression/cli-help/exportShmSingleCellTrees.txt
@@ -10,21 +10,24 @@ Usage: mixcr exportShmSingleCellTrees [--include-one-chain-trees] [--only-observ
                                       [-rootsCountPerChain] [-treeHeight] [-nodeId] [-isObserved]
                                       [-parentId] [-distance (germline|mrca|parent)]... [-vHit]
                                       [-jHit] [-vGene] [-jGene] [-vFamily] [-jFamily] [-nFeature
-                                      <gene_feature> [(germline|mrca|parent)]]... [-allNFeatures
-                                      [(germline|mrca|parent)]]... [-aaFeature <gene_feature>
-                                      [(germline|mrca|parent)]]... [-allAAFeatures
-                                      [(germline|mrca|parent)]]... [-nFeatureImputed <gene_feature>
-                                      [(germline|mrca|parent)]]... [-allNFeaturesImputed
-                                      [<from_reference_point> <to_reference_point>]
-                                      [(germline|mrca|parent)]]... [-aaFeatureImputed
-                                      <gene_feature> [(germline|mrca|parent)]]...
-                                      [-allAAFeaturesImputed [<from_reference_point>
-                                      <to_reference_point>] [(germline|mrca|parent)]]... [-nLength
-                                      <gene_feature[,gene_feature]...> [(germline|mrca|parent)]]...
-                                      [-allNLength [(germline|mrca|parent)]]... [-aaLength
-                                      <gene_feature[,gene_feature]...> [(germline|mrca|parent)]]...
-                                      [-allAALength [(germline|mrca|parent)]]... [-nMutations
                                       <gene_feature> [(germline|mrca|parent)]
+                                      [withAlignmentGaps]]... [-allNFeatures
+                                      [(germline|mrca|parent)] [withAlignmentGaps]]... [-aaFeature
+                                      <gene_feature> [(germline|mrca|parent)]
+                                      [withAlignmentGaps]]... [-allAAFeatures
+                                      [(germline|mrca|parent)] [withAlignmentGaps]]...
+                                      [-nFeatureImputed <gene_feature> [(germline|mrca|parent)]]...
+                                      [-allNFeaturesImputed [<from_reference_point>
+                                      <to_reference_point>] [(germline|mrca|parent)]]...
+                                      [-aaFeatureImputed <gene_feature>
+                                      [(germline|mrca|parent)]]... [-allAAFeaturesImputed
+                                      [<from_reference_point> <to_reference_point>]
+                                      [(germline|mrca|parent)]]... [-nLength <gene_feature[,
+                                      gene_feature]...> [(germline|mrca|parent)]]... [-allNLength
+                                      [(germline|mrca|parent)]]... [-aaLength <gene_feature[,
+                                      gene_feature]...> [(germline|mrca|parent)]]... [-allAALength
+                                      [(germline|mrca|parent)]]... [-nMutations <gene_feature>
+                                      [(germline|mrca|parent)]
                                       [(substitutions|indels|inserts|deletions)]]...
                                       [-allNMutations [(germline|mrca|parent)]
                                       [(substitutions|indels|inserts|deletions)]]...
@@ -57,8 +60,10 @@ Usage: mixcr exportShmSingleCellTrees [--include-one-chain-trees] [--only-observ
                                       gene_feature]...>]
                                       [(substitutions|indels|inserts|deletions)]]...
                                       [-aaMutationsRate [<gene_feature[,gene_feature]...>]
-                                      [(substitutions|indels|inserts|deletions)]]... [-isotype
-                                      [(primary|subclass|auto)]]... [-cellId
+                                      [(substitutions|indels|inserts|deletions)]]... [-pN
+                                      [<gene_feature[,gene_feature]...>]]... [-pS [<gene_feature[,
+                                      gene_feature]...>]]... [-pNpS [<gene_feature[,gene_feature]...
+                                      >]]... [-isotype [(primary|subclass|auto)]]... [-cellId
                                       [(none|space|dash)]]... [-uniqueTagCount
                                       (Molecule|Cell|Sample)]... [-cellGroup] [-hasStops
                                       <gene_feature>]... [-isOOF <gene_feature>]... [-isProductive
@@ -84,8 +89,8 @@ separate columns. Initial data for building tree should contain cell data.
       --ids <id>[,<id>...]   Filter specific trees by id
       --chains <chains>      Export only trees that contains clones with specific chain (e.g. IGK,
                                IGL or IGH).
-  -p, --preset <preset>      Specify preset of export fields. Possible values: min, default.
-      -pf, --preset-file <presetFile>
+      --preset <preset>      Specify preset of export fields. Possible values: min, default.
+      --preset-file <presetFile>
                              Specify preset file of export fields
       --cell-type <cell_type>...
                              Export SHM trees for given cell type. By default all will be exported.
@@ -140,19 +145,19 @@ Possible fields to export
       -jGene                 Export best J hit gene name (e.g. TRBV12-3 for TRBV12-3*00)
       -vFamily               Export best V hit family name (e.g. TRBV12 for TRBV12-3*00)
       -jFamily               Export best J hit family name (e.g. TRBV12 for TRBV12-3*00)
-      -nFeature <gene_feature> [(germline|mrca|parent)]
+      -nFeature <gene_feature> [(germline|mrca|parent)] [withAlignmentGaps]
                              Export nucleotide sequence of specified gene feature.
                              If second arg is omitted, then feature will be printed for current
                                node. Otherwise - for corresponding `parent`, `germline` or `mrca`.
-      -allNFeatures [(germline|mrca|parent)]
+      -allNFeatures [(germline|mrca|parent)] [withAlignmentGaps]
                              Export nucleotide sequences for all covered gene features.
                              If first arg is omitted, then feature will be printed for current
                                node. Otherwise - for corresponding `parent`, `germline` or `mrca`.
-      -aaFeature <gene_feature> [(germline|mrca|parent)]
+      -aaFeature <gene_feature> [(germline|mrca|parent)] [withAlignmentGaps]
                              Export amino acid sequence of specified gene feature.
                              If second arg is omitted, then feature will be printed for current
                                node. Otherwise - for corresponding `parent`, `germline` or `mrca`.
-      -allAAFeatures [(germline|mrca|parent)]
+      -allAAFeatures [(germline|mrca|parent)] [withAlignmentGaps]
                              Export amino acid sequences for all covered gene features.
                              If first arg is omitted, then feature will be printed for current
                                node. Otherwise - for corresponding `parent`, `germline` or `mrca`.
@@ -308,6 +313,21 @@ Possible fields to export
                                Resolutions of wildcards in CDR3 are excluded from calculation.
                                Second parameter will filter mutations by type, by default no
                                filtering.
+      -pN [<gene_feature[,gene_feature]...>]
+                             Count of non-synonymous substitutions normalized by total count of
+                               possible non-synonymous substitutions. By default, will be used all
+                               covered features. For wildcards in VJJunction all possible
+                               combinations will be calculated and averaged.
+      -pS [<gene_feature[,gene_feature]...>]
+                             Count of synonymous substitutions normalized by total count of
+                               possible synonymous substitutions. By default, will be used all
+                               covered features. For wildcards in VJJunction all possible
+                               combinations will be calculated and averaged.
+      -pNpS [<gene_feature[,gene_feature]...>]
+                             Ration of pN to pS. In case of no mutations value will be absent.By
+                               default, will be used all covered features. For wildcards in
+                               VJJunction all possible combinations will be calculated and
+                               averaged. If pN or pS is zero, no value will be exported.
       -isotype [(primary|subclass|auto)]
                              Export isotype for IGH chains if it's can be distinguishable.
                                `primary` will resolve 'IgA', 'IgD', 'IgG', 'IgE', 'IgM'. `subtype`
diff --git a/regression/cli-help/exportShmTrees.txt b/regression/cli-help/exportShmTrees.txt
index e6a886ae2..db30bf4bc 100644
--- a/regression/cli-help/exportShmTrees.txt
+++ b/regression/cli-help/exportShmTrees.txt
@@ -26,9 +26,9 @@ data)
       --ids <id>[,<id>...]   Filter specific trees by id
       --chains <chains>      Export only trees that contains clones with specific chain (e.g. IGK,
                                IGL or IGH).
-  -p, --preset <preset>      Specify preset of export fields. Possible values: default,
+      --preset <preset>      Specify preset of export fields. Possible values: default,
                                defaultSingleCell, min.
-      -pf, --preset-file <presetFile>
+      --preset-file <presetFile>
                              Specify preset file of export fields
       --no-header            Don't print first header line, print only data
       --not-covered-as-empty Export not covered regions as empty text.
diff --git a/regression/cli-help/exportShmTreesWithNodes.txt b/regression/cli-help/exportShmTreesWithNodes.txt
index 3bbbdf0ab..868bd2036 100644
--- a/regression/cli-help/exportShmTreesWithNodes.txt
+++ b/regression/cli-help/exportShmTreesWithNodes.txt
@@ -17,12 +17,14 @@ Usage: mixcr exportShmTreesWithNodes [--split-by-tags (Molecule|Cell|Sample)] [-
                                      [-dFamilies] [-jFamilies] [-cFamilies] [-vAlignment]
                                      [-dAlignment] [-jAlignment] [-cAlignment] [-vAlignments]
                                      [-dAlignments] [-jAlignments] [-cAlignments] [-nFeature
-                                     <gene_feature> [(germline|mrca|parent)]]... [-allNFeatures
-                                     [(germline|mrca|parent)]]... [-qFeature <gene_feature>]...
-                                     [-allQFeatures [<from_reference_point>
+                                     <gene_feature> [(germline|mrca|parent)]
+                                     [withAlignmentGaps]]... [-allNFeatures
+                                     [(germline|mrca|parent)] [withAlignmentGaps]]... [-qFeature
+                                     <gene_feature>]... [-allQFeatures [<from_reference_point>
                                      <to_reference_point>]]... [-aaFeature <gene_feature>
-                                     [(germline|mrca|parent)]]... [-allAAFeatures
-                                     [(germline|mrca|parent)]]... [-nFeatureImputed <gene_feature>
+                                     [(germline|mrca|parent)] [withAlignmentGaps]]...
+                                     [-allAAFeatures [(germline|mrca|parent)]
+                                     [withAlignmentGaps]]... [-nFeatureImputed <gene_feature>
                                      [(germline|mrca|parent)]]... [-allNFeaturesImputed
                                      [<from_reference_point> <to_reference_point>]
                                      [(germline|mrca|parent)]]... [-aaFeatureImputed <gene_feature>
@@ -82,17 +84,20 @@ Usage: mixcr exportShmTreesWithNodes [--split-by-tags (Molecule|Cell|Sample)] [-
                                      [-nMutationsRate [<gene_feature[,gene_feature]...>]
                                      [(substitutions|indels|inserts|deletions)]]...
                                      [-aaMutationsRate [<gene_feature[,gene_feature]...>]
-                                     [(substitutions|indels|inserts|deletions)]]... [-geneLabel
-                                     <label>]... [-isotype [(primary|subclass|auto)]]...
-                                     [-tagCounts] [-cellId [(none|space|dash)]]... [-tags
-                                     (Molecule|Cell|Sample)]... [-uniqueTagCount
-                                     (Molecule|Cell|Sample)]... [-uniqueTagFraction
-                                     (Molecule|Cell|Sample)]... [-cellGroup] [-rankByTag
-                                     (Molecule|Cell|Sample)]... [-hasStops <gene_feature>]...
-                                     [-isOOF <gene_feature>]... [-isProductive [<gene_feature>]]...
-                                     [-biochemicalProperty <gene_feature> <property>
-                                     [(germline|mrca|parent)]]... [-baseBiochemicalProperties
-                                     <gene_feature> [(germline|mrca|parent)]]... [--use-local-temp]
+                                     [(substitutions|indels|inserts|deletions)]]... [-pN
+                                     [<gene_feature[,gene_feature]...>]]... [-pS [<gene_feature[,
+                                     gene_feature]...>]]... [-pNpS [<gene_feature[,gene_feature]...
+                                     >]]... [-geneLabel <label>]... [-isotype
+                                     [(primary|subclass|auto)]]... [-tagCounts] [-cellId
+                                     [(none|space|dash)]]... [-tags (Molecule|Cell|Sample)]...
+                                     [-uniqueTagCount (Molecule|Cell|Sample)]...
+                                     [-uniqueTagFraction (Molecule|Cell|Sample)]... [-cellGroup]
+                                     [-rankByTag (Molecule|Cell|Sample)]... [-hasStops
+                                     <gene_feature>]... [-isOOF <gene_feature>]... [-isProductive
+                                     [<gene_feature>]]... [-biochemicalProperty <gene_feature>
+                                     <property> [(germline|mrca|parent)]]...
+                                     [-baseBiochemicalProperties <gene_feature>
+                                     [(germline|mrca|parent)]]... [--use-local-temp]
                                      [--force-overwrite] [--no-warnings] [--verbose] [--help]
                                      [[--filter-in-feature <gene_feature>] [--pattern-max-errors
                                      <n>] (--filter-aa-pattern <pattern> | --filter-nt-pattern
@@ -111,8 +116,8 @@ root if no single cell data)
       --ids <id>[,<id>...]   Filter specific trees by id
       --chains <chains>      Export only trees that contains clones with specific chain (e.g. IGK,
                                IGL or IGH).
-  -p, --preset <preset>      Specify preset of export fields. Possible values: min, default.
-      -pf, --preset-file <presetFile>
+      --preset <preset>      Specify preset of export fields. Possible values: min, default.
+      --preset-file <presetFile>
                              Specify preset file of export fields
       --no-header            Don't print first header line, print only data
       --not-covered-as-empty Export not covered regions as empty text.
@@ -211,11 +216,11 @@ Possible fields to export
       -dAlignments           Export all D alignments (only for nodes with clones)
       -jAlignments           Export all J alignments (only for nodes with clones)
       -cAlignments           Export all C alignments (only for nodes with clones)
-      -nFeature <gene_feature> [(germline|mrca|parent)]
+      -nFeature <gene_feature> [(germline|mrca|parent)] [withAlignmentGaps]
                              Export nucleotide sequence of specified gene feature.
                              If second arg is omitted, then feature will be printed for current
                                node. Otherwise - for corresponding `parent`, `germline` or `mrca`.
-      -allNFeatures [(germline|mrca|parent)]
+      -allNFeatures [(germline|mrca|parent)] [withAlignmentGaps]
                              Export nucleotide sequences for all covered gene features.
                              If first arg is omitted, then feature will be printed for current
                                node. Otherwise - for corresponding `parent`, `germline` or `mrca`.
@@ -229,11 +234,11 @@ Possible fields to export
                                FR3`, `-qFeature CDR3`, `-qFeature FR4`.
                              By default, boundaries will be got from analysis parameters if
                                possible or `FR1Begin FR4End` otherwise. (only for nodes with clones)
-      -aaFeature <gene_feature> [(germline|mrca|parent)]
+      -aaFeature <gene_feature> [(germline|mrca|parent)] [withAlignmentGaps]
                              Export amino acid sequence of specified gene feature.
                              If second arg is omitted, then feature will be printed for current
                                node. Otherwise - for corresponding `parent`, `germline` or `mrca`.
-      -allAAFeatures [(germline|mrca|parent)]
+      -allAAFeatures [(germline|mrca|parent)] [withAlignmentGaps]
                              Export amino acid sequences for all covered gene features.
                              If first arg is omitted, then feature will be printed for current
                                node. Otherwise - for corresponding `parent`, `germline` or `mrca`.
@@ -471,6 +476,21 @@ Possible fields to export
                                Resolutions of wildcards in CDR3 are excluded from calculation.
                                Second parameter will filter mutations by type, by default no
                                filtering.
+      -pN [<gene_feature[,gene_feature]...>]
+                             Count of non-synonymous substitutions normalized by total count of
+                               possible non-synonymous substitutions. By default, will be used all
+                               covered features. For wildcards in VJJunction all possible
+                               combinations will be calculated and averaged.
+      -pS [<gene_feature[,gene_feature]...>]
+                             Count of synonymous substitutions normalized by total count of
+                               possible synonymous substitutions. By default, will be used all
+                               covered features. For wildcards in VJJunction all possible
+                               combinations will be calculated and averaged.
+      -pNpS [<gene_feature[,gene_feature]...>]
+                             Ration of pN to pS. In case of no mutations value will be absent.By
+                               default, will be used all covered features. For wildcards in
+                               VJJunction all possible combinations will be calculated and
+                               averaged. If pN or pS is zero, no value will be exported.
       -geneLabel <label>     Export gene label (i.e. ReliableChain) (only for nodes with clones)
       -isotype [(primary|subclass|auto)]
                              Export isotype for IGH chains if it's can be distinguishable.
diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/ExportUtil.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/ExportUtil.kt
index c615a4901..1e6b285aa 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/ExportUtil.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/ExportUtil.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:
@@ -65,7 +65,7 @@ fun <T : Any> FieldExtractorsFactory<T>.addOptionsToSpec(
     if (this is FieldExtractorsFactoryWithPresets) {
         spec.addOption(
             OptionSpec
-                .builder("-p", "--preset")
+                .builder("--preset")
                 .description("Specify preset of export fields. Possible values: \${COMPLETION-CANDIDATES}.")
                 .order(50_000 - 300)
                 .required(false)
@@ -82,7 +82,7 @@ fun <T : Any> FieldExtractorsFactory<T>.addOptionsToSpec(
         )
         spec.addOption(
             OptionSpec
-                .builder("-pf", "--preset-file")
+                .builder("--preset-file")
                 .description("Specify preset file of export fields")
                 .order(50_000 - 200)
                 .required(false)