I am having thousands of samples (DNA barcoded) for species confirmation (False positive or True positive species). This species confirmation is to be done on distance based and tree based methods.
In case of tree based methods, various phylogenetic models (NJ, Parsimony, Bayes) generated trees in 'Newick' format . Using these newick files as an input, can anyone suggest a software, R code or perl code that can extract list of species forming monophyla (True species) or paraphyla (False positive species)?
(I have done this in case of distance based method using R package 'Ad-hoc').
You can do that sort of thing with the SPIDER package in R. http://spider.r-forge.r-project.org/SpiderWebSite/spider.html
Agreed with Ding He on ETE.
Check under ETE Documentation > Library> MasterTree module for commands like get_monophyly().
T-REX is web server for phylogenetic (trees and networks).
Bioperl project is another.
Bioconductor project based on R, is an open source. It allow access to tools and methods for the analysis and comprehension of genomic data.
Try the function is.monophyletic in the R package ape. It takes the tree and the name(s) of the tips for which you are trying to assess monophyly. Depending on your input, you should be able to incorporate this in a loop to assess the monophyly of many taxa or across many trees.
I was going to suggest is.monophyletic on ape (R) either, but since someone has already, I'll just add up you should unroot trees first. It helps avoid some problems.
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