MCMCTREE problem: Error in sequence data file: E at 61 seq 1.

[Y DD]

I don't know why erros

I checked and make sure that NO " E"

maybe you can download the annex and try again, thank you vermuch!

[Sishuo Wang]

Hi there,

As indicated in the err msg, for some reason, paml thinks ur input alignment is in the sequential phylip format but ur phylip file is in an interleaved phylip format. See the following screenshot. In the 1st line it's indicated there r 30348 sites but then we come into the next line which is "ea_NC_042778_1"; that's why you got the err msg "E at 61 seq 1". I am unsure how to convert it into a correct interleaved format but you can use the correct sequential format, i.e., to merge diff parts of the same seq into the same line. For example, see https://lorenzogatti.me/2017-ACGT-Tutorials/docs/howto_Format_Data/.

best,

sishuo

[Y DD]

I tried, and it worked, thank you very much！！！thank you！！！

[Y DD]

I don't konw why it didn't worked again

'trimal  -in 84.fas -out 84.phy -phylip_paml'

'perl Fasta2Phylip.pl 84.fas 84.bad.phy'

[Y DD]

ALL these six files

Perhaps you could take a look at it when you have time? I would be deeply grateful for any help

[Y DD]

No problem now, I found that there were no errors when 'ndata = 1' was set in the 'mcmctree.ctl' file