Hello,
I need to generate a matrices file that "contains a list of m distance matrices in PHYLIP format (lower triangular or square)" for m number of loci. This is one of the input files for ERaBLE: Evolutionary Rates and Branch Length Estimation. I have a large number of loci and I would prefer a method that can batch process files, preferably one which can generate the output files in PHYLIP format.
My goal is to identify fast- and slow-evolving genes. I am evidently using ERaBLE for the first time. If anyone has suggestions regarding its usage for the estimation of evolutionary rates, they are welcome!
I normally use the program ClustalW under linux to generate both an alignment and a distance matrix.
The linux command that produces an alignment followed by the distance matrix on the terminal screen is the following: clustalw -outputtree=dist -tree -infile=test.aln;l test.aln;l test.dst'. The file test.aln contains the sequences in fastA format and results are written to the filenames test.aln and test.dst.
Please note that the letters l in the command line represent an alias. If the alias does not work on your linux terminal replace the letter l with the linux command "less".
Thank you so much for such a detailed answer! This will work perfectly for me.
- Badges
- Science topic
- Similar topics
- Mathematical Sciences
- Statistics
- Probability
- Probability Theory
- Reliability