This software allows to identify sequence regions of multiple protein-coding gene alignments that exhibit local deviation from stationarity for different physico-chemical amino acid properties and that can be responsible for misleading phylogenetic inferences.
Please cite: Fedrigo, O., D.C. Adams, and G.J.P. Naylor. (2005) DRUIDS – Detection of Regions with Unexpected Internal Deviation from Stationarity. J. Exp. Zoolog. Part B Mol. Dev. Evol. 304(2): 119-128.
Three versions are available:
- Windows vesion (Druids_Setup.exe), not tested after windows XP
- Mac OSX version (Druids.dmg), not tested after OSX 10.5
- Python version (pyDruids.py), command line version. See below
pyDruids.py -f inputFileName -w windowSize -a attribute -o outputFileName -b nreplicates -p percent -g geneticCode -m fillGaps
requires Bio Python to be installed.
inputFileName any of the following formats: phylip, fasta, nexus (should ends with .phy or .phylip or .fasta or .nex or.nexus) bases should be all upper case: A ,C ,G or T assume your data is in frame and its length is /3 multiple
windowSize minimum window size=3 maximum wiwdow size= half the the sequence length default= 21
attribute comma separated attributes any of GA,GT,AT,AC,TC,GC for %base content H: hydrophobicity V: colume C: charge default= H
outputFileName will output: _windows.out: only significant windows _DFS.out: all the values default= DruidsOutput
nreplicates number of codon bootstrap replicates default= 100
percent significant cutoff in the resampled distribution to call significant windows default= 0.05
geneticCode for now, are only available: mammalMt and universal default= universal
fillGaps FALSE: it will assign the mean attribute value of the window to this site for unknown characters (e.g. gaps, lower case, N) TRUE: it will replace gaps by the most common base if the character is unknown default= FALSE