phasty.wrapper#

A module wraps the major programs of PHAST.

Functions

all_dists(*args, **kwargs)

Run command and return the stdout.

base_evolve(*args, **kwargs)

Run command and return the stdout.

choose_lines(*args, **kwargs)

Run command and return the stdout.

clean_genes(*args, **kwargs)

Run command and return the stdout.

cons_entropy(*args, **kwargs)

Run command and return the stdout.

convert_coords(*args, **kwargs)

Run command and return the stdout.

display_rate_matrix(*args, **kwargs)

Run command and return the stdout.

dless(*args, **kwargs)

Run command and return the stdout.

dless_p(*args, **kwargs)

Run command and return the stdout.

dm_translate_to_realigned(*args, **kwargs)

Run command and return the stdout.

dmcompare(*args, **kwargs)

Run command and return the stdout.

dmcondition(*args, **kwargs)

Run command and return the stdout.

dmotif(*args, **kwargs)

Run command and return the stdout.

dmsample(*args, **kwargs)

Run command and return the stdout.

dmsimulate(*args, **kwargs)

Run command and return the stdout.

draw_tree(*args, **kwargs)

Run command and return the stdout.

eval_predictions(*args, **kwargs)

Run command and return the stdout.

exoniphy(*args, **kwargs)

Run command and return the stdout.

hmm_train(*args, **kwargs)

Run command and return the stdout.

hmm_tweak(*args, **kwargs)

Run command and return the stdout.

hmm_view(*args, **kwargs)

Run command and return the stdout.

indel_fit(*args, **kwargs)

Run command and return the stdout.

indel_history(*args, **kwargs)

Run command and return the stdout.

maf_parse(*args, **kwargs)

Run command and return the stdout.

make_hky(*args, **kwargs)

Run command and return the stdout.

mod_freqs(*args, **kwargs)

Run command and return the stdout.

msa_diff(*args, **kwargs)

Run command and return the stdout.

msa_split(*args, **kwargs)

Run command and return the stdout.

msa_view(*args, **kwargs)

Run command and return the stdout.

pbs_decode(*args, **kwargs)

Run command and return the stdout.

pbs_encode(*args, **kwargs)

Run command and return the stdout.

pbs_score_matrix(*args, **kwargs)

Run command and return the stdout.

pbs_train(*args, **kwargs)

Run command and return the stdout.

phast_bias(*args, **kwargs)

Run command and return the stdout.

phast_cons(*args, **kwargs)

Run command and return the stdout.

phast_motif(*args, **kwargs)

Run command and return the stdout.

phast_odds(*args, **kwargs)

Run command and return the stdout.

phylo_boot(*args, **kwargs)

Run command and return the stdout.

phylo_fit(*args, **kwargs)

Run command and return the stdout.

phylo_p(*args, **kwargs)

Run command and return the stdout.

prequel(*args, **kwargs)

Run command and return the stdout.

refeature(*args, **kwargs)

Run command and return the stdout.

stringiphy(*args, **kwargs)

Run command and return the stdout.

tree_gen(*args, **kwargs)

Run command and return the stdout.

tree_doctor(*args, **kwargs)

Run command and return the stdout.