phyrn

PHYlogenetic ReconstructioN (PHYRN) PHYRN provides a set of tools to accurately infer evolutionary relationship in highly divergent protein families/superfamilies. PHYRN relies on a PSSM-driven approach, and results from various synthetic and biological data sets show that PHYRN provides more accurate and robust inference of evolutionary history. Benchmarking studies show that PHYRN is a reliable phylogenetic inference tool in "twilight-zone" of sequence similarity. Current version of PHYRN is designed to handle only amino acid sequences for phylogenetic inference. The software is distributed as a collection of scripts written in Python, and Java. Python scripts require libraries numpy, Biopython to function properly. Current Version We have updated the downloads version with version 1.7.2. It includes support for resampling and minor bug fixes regarding some issues with input matrix file formats durin

phyrn-1.7.2
changeTreeQueryName.jar
chopFL.py
genCSMAT.py
genEUCLID.py
genPSSM.pl
genSUMMARY.jar
Makefile
phyrn_phylip.h
PHYRN_user_manual.pdf
phyrnboot.c
pssmgen.py
pssmgen_array.py
readme.txt