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Add comment re. failing msaMuscle()

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hyginn 2017-11-20 18:59:54 -05:00
parent f747f7896e
commit 9a987c22be
1 changed files with 5 additions and 3 deletions
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8
BIN-PHYLO-Data_preparation.R
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@ -32,8 +32,8 @@
#TOC> 1 Preparations 41 #TOC> 1 Preparations 41
#TOC> 2 Fetching sequences 78 #TOC> 2 Fetching sequences 78
#TOC> 3 Multiple Sequence Alignment 119 #TOC> 3 Multiple Sequence Alignment 119
#TOC> 4 Reviewing and Editing Alignments 136 #TOC> 4 Reviewing and Editing Alignments 138
#TOC> 4.1 Masking workflow 152 #TOC> 4.1 Masking workflow 154
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -126,10 +126,12 @@ tail(APSI)
APSESSet <- AAStringSet(APSI) APSESSet <- AAStringSet(APSI)
APSESMsa <- msaMuscle(APSESSet, order = "aligned") APSESMsa <- msaMuscle(APSESSet, order = "aligned")
# Nb. msaMuscle() sometimes fails - reproducibly, but I am not sure why. If
# that happens in your case, just use msaClustalOmega() instead.
# inspect the alignment. # inspect the alignment.
writeALN(APSESMsa) writeALN(APSESMsa)
# What do you think? Is this a good alignment for phylogenetic inference? # What do you think? Is this a good alignment for phylogenetic inference?