I use MEGA 5 (http://www.megasoftware.net/) for MacOS to calculate phylogenetic distancies basen on non-synonimous substitutions. However, in order to implement such calculations into my pipeline, I need to call this algorithms from UNIX-like console. So, can anyone help me?
Thanks in advance.
Phylip's dnadist or paup* for general use
for syn and nsyn dists, you could try SNAP or HyPhy
Depends on the type of distances (mainly, which models) you want. EMBOSS' distmat is a good CLI program for a pipeline, I think, and does both uncorrected and corrected (by a choice from a few different models) distances.
http://emboss.sourceforge.net/apps/release/6.4/emboss/apps/distmat.html
Another possibility would be to use codeml from the PAML package (http://abacus.gene.ucl.ac.uk/software/paml.html) that allows you to estimate dN from amino-acid-constrained DNA sequences (i.e it uses a codon based model). If your pipeline is simple but takes long time or requires computational resources, you can try iPlant's discovery environment (http://www.iplantcollaborative.org/discover/discovery-environment)
If you have the phylogenetic tree, CodeML from PAML is easy to implement in pipeline to recompute the branch lengths.
If you need to build the tree topology, you could use PhyML or RAxML.
I'd use DNAdist and Protdist, both availble from Phylip
http://evolution.genetics.washington.edu/phylip.html
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