Modified doc

evolbioinfo · Dec 22, 2017 · 045017d · 045017d
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diff --git a/docs/commands/brlen.md b/docs/commands/brlen.md
@@ -100,7 +100,7 @@ should output:
 ```
 
 ```
-gotree generate yuletree -s 10 -n 10 | gotree clear lengths
+gotree generate yuletree -s 10 -n 10 | gotree brlen clear
 ```
 
 should output :
@@ -120,7 +120,7 @@ should output :
 2. Assign random lengths to a random tree
 ```
 gotree generate yuletree -s 10 -o outtree1.nw
-gotree randbrlen -i outtree.nw -s 13 -o outtree2.nw
+gotree brlen setrand -i outtree.nw -s 13 -o outtree2.nw
 gotree draw svg -w 200 -H 200  -i outtree1.nw -o commands/randbrlen_1.svg
 gotree draw svg -w 200 -H 200  -i outtree2.nw -o commands/randbrlen_2.svg
 ```
@@ -135,7 +135,7 @@ Initial random Tree               | Random lengths
 ```
 gotree generate yuletree -s 10 -l 100 -o outtree.nw
 gotree draw svg -r -w 200 -H 200 --no-tip-labels -i outtree.nw -o commands/minbrlen_1.svg
-gotree minbrlen -i outtree.nw -l 0.1 | gotree draw svg -r -w 200 -H 200 --no-tip-labels -o commands/minbrlen_2.svg
+gotree brlen setmin -i outtree.nw -l 0.1 | gotree draw svg -r -w 200 -H 200 --no-tip-labels -o commands/minbrlen_2.svg
 ```
 
 Random Tree                          | Min brlen tree

diff --git a/docs/commands/clear.md b/docs/commands/clear.md
diff --git a/docs/commands/comment.md b/docs/commands/comment.md
@@ -37,7 +37,7 @@ Global Flags:
 
 * Removing node comments from an input tree
 ```
-echo "(t1[c1],t2[c2],(t3[c3],t4[c4])[c5]);" | gotree clear comments
+echo "(t1[c1],t2[c2],(t3[c3],t4[c4])[c5]);" | gotree comment clear
 ```
 
 Should print:

diff --git a/docs/commands/support.md b/docs/commands/support.md
@@ -52,7 +52,7 @@ Global Flags:
 
 1. Removing branch supports from a set of 10 trees
 ```
-gotree generate yuletree -s 10 -n 10 | gotree clear lengths | gotree randsupport -s 10
+gotree generate yuletree -s 10 -n 10 | gotree brlen clear | gotree support setrand -s 10
 ```
 
 Should give: 
@@ -70,7 +70,7 @@ Should give:
 ```
 
 ```
-gotree generate yuletree -s 10 -n 10 | gotree clear lengths | gotree randsupport -s 10 | gotree clear supports
+gotree generate yuletree -s 10 -n 10 | gotree brlen clear | gotree support setrand -s 10 | gotree support clear
 ```
 
 Should produce:
@@ -91,7 +91,7 @@ Should produce:
 2. Assigning random supports to a random tree and highlight branches with support > 0.5
 ```
 gotree generate yuletree -s 10 -o outtree1.nw
-gotree randsupport -i outtree.nw -s 12 -o outtree2.nw
+gotree support setrand -i outtree.nw -s 12 -o outtree2.nw
 gotree draw svg -w 200 -H 200  -i outtree1.nw -o commands/randsupport_1.svg
 gotree draw svg -w 200 -H 200  -i outtree2.nw --with-branch-support --support-cutoff 0.5 -o commands/randsupport_2.svg
 ```