hmm_train - Estimate the transition probabilities of an HMM, based
on multiple -g <gff_fname_list> [OPTIONS] > out.hmm
Estimate the transition probabilities of an HMM, based on multiple
alignments, sequence annotations, and a category map.
-m <msa_fname_list>
- List of multiple sequence alignment files. Currently, in testing mode, the
list must be of length one.
-c <category_map_fname>
- File defining mapping of feature types to category numbers.
-g <gff_fname_list>
- Files in GFF defining sequence features to be used in labeling sites.
Frame of reference of feature indices is determined feature-by-feature
according to
- 'seqname' attribute.
- Filenames must correspond in number and order
- to the elements of <msa_fname_list>.
-M <msa_length_list>
- (Mutually exclusive with -m) Assume alignments of the specified
lengths (comma-separated list) and do not not attempt to map the
coordinates in the specified GFFs (assume they are in the desired
coordinate frame). This option allows an HMM to be trained directly from
GFFs, without alignments. Not permitted with -I.
-i PHYLIP|FASTA|MPM|SS
- (default SS) Alignment format.
-R <tag>
- Before estimating transition probabilities, group features by <tag>
(e.g., "transcript_id" or "exon_id") and reverse
complement segments of the alignment corresponding to groups on the
reverse strand. Groups must be non-overlapping (see refeature
--unique).
-I <indel_cat_list>
- Model indels for specified
categories.
- To have
- nonzero probability for the states corresponding to a specified category
range, indels must be "clean" (nonoverlapping), must be
assignable by parsimony to a single branch in the phylogenetic tree, and
must have lengths that are exact multiples of the category range size.
Avoid -G with this option. If used in training mode, requires
-T.
-t <tree_fname>
- Use the specified tree topology when training for indels.
-n <nseqs>
- Train an indel model for <nseqs> sequences, despite that the
training alignment has a different number. All (non-trivial) gap patterns
are assumed to be equally frequent.
-q
- Proceed quietly (without updates to stderr).
-h
- Print this help message and exit.