Merge branch 'master' of github.com:fredericlemoine/goalign

evolbioinfo · Jul 3, 2017 · 8cdcef7 · 8cdcef7
2 parents 1264647 + fa90c05
commit 8cdcef7
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diff --git a/docs/commands/clean.md b/docs/commands/clean.md
@@ -30,7 +30,7 @@ Global Flags:
 
 * Generating a gapped alignment, and removing positions having at least one gap:
 ```
-goalign random -s 10 | goalign shuffle gaps -n 1 -r 0.1 -s 10 |  goalign clean
+goalign random -s 10 | goalign mutate gaps -n 1 -r 0.1 -s 10 |  goalign clean
 ```
 
 Should give on stdout:

diff --git a/docs/commands/unalign.md b/docs/commands/unalign.md
@@ -42,9 +42,9 @@ Global Flags:
 * Generating random alignment, adding 50% gaps in 50% of the sequences, and unaligning it:
 ```
 # Gapped alignment
-goalign random -s 10 -p | goalign shuffle gaps -s 10 -p
+goalign random -s 10 -p | goalign mutate gaps -s 10 -p
 # Gapped alignment => unaligned
-goalign random -s 10 -p | goalign shuffle gaps -s 10 -p | goalign unalign -p
+goalign random -s 10 -p | goalign mutate gaps -s 10 -p | goalign unalign -p
 ```
 Should output:
 ```