Hi all,

I have been working on a comparative genomic analysis of 15 species with their peptide sequence files. r8s is being employed to obtain an ultrametric tree for the Expansion/Contraction gene families. I have used the Orthofinder software and the online website named timetree to generate the input file of cafetutorial_prep_r8s.py to prepare the input file of r8s. Below is the shell command line:

${python3} ${cafetutorial_prep_r8s} -i ${SpeciesTree_rooted} -s 1358452 -p 'pun,gas' -c 25.4 -o r8s_ctl_file.txt

And below is the content of r8s_ctl_file.txt:

Then I typed the below command line to run r8s:

${r8s} -b -f r8s_ctl_file.txt > r8s_tmp.txt

The issue came out in the r8s_tmp.txt:

Although I can get an ultrametric tree from the r8s_tmp.txt file, I do not have confidence to accept it.

tree nj_tree = (((((((lan:9.462700,moa:9.462700):72.154297,((((cyc:47.461888,tra:47.461888):13.773615,((gas:25.400000,pun:25.400000)pungas:32.723144,ana:58.123144):3.112358):12.100030,umb:73.335533):2.912089,cot:76.247621):5.369376):18.645923,ser:100.262920):17.375916,(poe:91.401128,ory:91.401128):26.237709):15.635127,cyn:133.273964):105.913809,dan:239.187773):92.452473,lep:331.640245);

Any help will be very appreciated!