[R] merging nexus sequence files

nikki22 nikkiharrison at me.com
Fri Sep 16 00:00:22 CEST 2011

Hi, newbie here,

I was wondering if anyone can out, I have checked through the help archives
but cannot find my answer.

I have three nexus files mostly with the same taxa but some are different. I
want to concatenate the DNA sequences from these three files into one large
nexus file but I cannot seem to accomplish it!

This is an example:

taxon1 aaggttcc
taxon2 aagtttcg
taxon3 aaggttcc

taxon2 ctgctg
taxon3 ctggtc
taxon4 ctgctg

taxon1 ggttggtta
taxon2 ggttggttc
taxon4 ggttggttc

this is what i want to end up with (where ? means missing data) in nexus

taxon1 aaggttcc??????ggttggtta
taxon2 aagtttcgctgctgggttggttc
taxon3 aaggttccctggtc????????
taxon4 ??????????????ggttggttc

Thanks in advance for any help!

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