|
parse_basics(lines,
results)
Parse the basic information that should be present in most codeml
output files. |
source code
|
|
|
parse_nssites(lines,
results,
multi_models)
Determine which NSsites models are present and parse them. |
source code
|
|
|
parse_model(lines,
results)
Parse an individual NSsites model's results. |
source code
|
|
|
parse_siteclass_proportions(line_floats)
For models which have multiple site classes, find the proportion of
the alignment assigned to each class. |
source code
|
|
|
parse_siteclass_omegas(line,
site_classes)
For models which have multiple site classes, find the omega estimated
for each class. |
source code
|
|
|
parse_clademodelc(branch_type_no,
line_floats,
site_classes)
Parse results specific to the clade model C. |
source code
|
|
|
parse_branch_site_a(foreground,
line_floats,
site_classes)
Parse results specific to the branch site A model. |
source code
|
|
|
parse_pairwise(lines,
results)
Parse results from pairwise comparisons. |
source code
|
|
|
parse_distances(lines,
results)
Parse amino acid sequence distance results. |
source code
|
|