Is there any way to customise the colour codes for multiple-sequence alignment (MSA)?
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10 weeks ago
Kumar ▴ 50

I have a fasta file as shown below, rvd.fasta

>t1
NI-NG-NR-NN-NG-HD-HD
>t_temp5
NG-NG-NI-N*-NR-NI-NN-NG-NG-HD
>tal8
NG-NG-NI-N*-ND-NI-NN-NG-NG-H*-NH-NI


I have a newick file as follows, tree.newick

(tal8:0.49999997,t_temp5:0.47298786,t1:28.37858179);


I need to visualise both the tree and rvd.fasta file (multiple-sequence alignment file) together. The expected output illustration should be similar to the model_picture shown here,

With the help of my previous post and ete toolkit I have learned how to combine phylogenetic tree with multiple-sequence alignment, but here the multiple-sequence alignment is different from the usual msa pattern. Therefore, please help me to do the same.

alignment Python genomics R phylogeny • 145 views