codeml: error in tree file

[Jens Boyen]

Hi all,

I am trying to run different models on three different genes using codeML. I used MUSCLE to create alignment files and RaxML to generate newick tree files. I avoided bootstrap labels but retained branch lengths.

For the first two genes (<50 sequences), I added outgroups when creating my RaxML trees, and managed to run codeML (both SM and BSM). For the third gene (elovl) (245 seqs), I did not include an outgroup when running RaxML (e.g. unrooted tree), otherwise all steps are similar to the first two genes. For this gene, codeML keeps failing, i assume when loading the tree file, saying "Species GHXK01177303.1_Platychelipus_littoralis_elovl1a_cds?" (the name of the second sequence in the seqfile).

I tried solving the problem by removing the branch lengths in the Newick file, but the error remains.

I also 'rooted' the newick tree using midpoint rooting in MEGA, but now the error says:

Species SRP063962_comp83773_c0_seq4_Pseudocalanus_acuspes_cds?

In attachment the seqfile, treefile (unrooted, with branch lengths), treefile "nobl" (unrooted, branch lengths removed), and treefile "nobl_mp" (midpoint rooted, branch lengths removed).

Thanks a lot in advance for helping me out!

Kind regards,

Jens Boyen

[Sishuo Wang]

Hi Jens,

I saw no problems using v4.10. Could u pls try it? I specified "codon" as the seqtype in codeml.ctl when using codeml. You might want to upload also the .ctl file next time.

Sishuo