Phylip (->Prodist) Command Line Wrapper In Biopython

Question

[Thaman]

Phylip has different applications for different phylogency purposes. Can anyone suggest me how to operate PHYLIP suppose(consense, dnaml,protdist) through commandline in biopython. Each applications has got its own different parameters, how can i handle them?

Answer 1

[Paulo Nuin]

BioPython doesn't have a direct wrapper to Phylip's apps, but it has wrappers to EMBOSS' versions of Phylip. Check BioPython's tutorial on how to accomplish it.

[Eric T.]

Also, to use the EMBOSS versions of Phylip you need to install a separate set of extensions to EMBOSS, called EMBASSY. You want PHYLIPNEW

Then the instructions for using Bio.Emboss.Applications will work.

[Thaman]

I succeed in getting Alignment output from MUSCLE. How can i pass command line argument to phylip application suppose i want to use protdist? keeping in mind that phylip doesn't have biopython wrapper like emboss does. I have been stuck on this problem for atleast 2 days searching command line wrapper for inputting and outputting results between applications.

[Paulo Nuin]

Please, read this comment carefully. BioPython doesn't have a direct wrapper to Phylip's apps, but it has a wrapper to the EMBOSS version of the same apps. Check out the link, and try to build something around these wrappers to calculate trees.