- do_outgroup(OUTGROUP, NUMSEQ, comfile, h_msgfile)
- Make sure OUTGROUP is not greater than NUMSEQ
- Read first line of a Phylip file to find out how many sequences there are
- jumble(comfile, h_msgfile, NUMJUM)
- Jumble - When multiple datasets are analyzed, protpars automatically
jumbles, and prompts for a random number seed for jumbling. Otherwise,
jumbling must be explicitly set.
- merge_msg(outfile_path, consense=True, extra=False)
- Merge messages from MSGFILE to the outfile generated by a Phylip program.
If extra is included as a parameter, this appends a message indicating
that the output is a consensus tree, whose branch lengths are the
bootstrap values, NOT the actual branch lengths.
- Generate a random integer as needed by Phylip programs.
These numbers are used by Phylip programs as seeds for a random
number stream. They must be odd, in the form 4n + 1. Return value
is an integer between 0 and 2e16 -1 (which is 65535). Although the
Phylip Main document claims that 32-bit random numbers are acceptible,
at least one program, PARS, will only take 16-bit random numbers
- seqboot(INFILE, DATATYPE, RSEED, METHOD, REPLICATES, PERCENT, BLOCKSIZE, OUTWEIGHTS, OUTFORMAT, OUTFILE)
- Run Seqboot. Notes: SEQBOOT reads interleaved sequences by default, but can read
sequential files using the "I" setting. By default, SEQBOOT
writes datasets to outfile, but will write weights to 'outweights'
if you set the "S" option. Weight files are always sequential.
- stdresample(METHOD, PERCENT, REPLICATES, BLOCKSIZE, h_msgfile, DATATYPE, OUTFORMAT)
- Run SEQBOOT to generate resampled datasets. Output is weights, used by Phylip programs
to generate datasets on the fly. If you want SEQBOOT to generate actual datasets instead of
weights, use weightless_resample instead.
- ufn(UFN, TEMPDIR, infile=True)
- Make sure that treefile begins with number of trees on first
line of file. If first line in file has parentheses, the
number must be added.
- weightless_resample(METHOD, PERCENT, REPLICATES, BLOCKSIZE, msgfile_h, DATATYPE, OUTFORMAT)
- Generate terminal input for running seqboot to generate randomized sequence files, rather than weight files
and run seqboot