Provided by: phast_1.4+dfsg-1_amd64 
NAME
msa_split - Partitions a multiple sequence alignment either at designated
DESCRIPTION
Partitions a multiple sequence alignment either at designated columns, or according to specified category
labels, and outputs sub-alignments for the partitions. Optionally splits an associated annotations file.
EXAMPLE
(See below for details on options)
1. Read an alignment for a whole human chromosome from a MAF file and extract sub-alignments in 1Mb
windows overlapping by 1kb. Use sufficient statistics (SS) format for output (can be used by phyloFit,
phastCons, or exoniphy). Set window boundaries between alignment blocks, if possible.
msa_split chr1.maf --refseq chr1.fa --in-format MAF --windows 1000000,1000 --out-format SS
--between-blocks 5000 --out-root chr1
(Windows will be defined using the coordinate system of the first sequence in the alignment, assumed to
be the reference sequence; output will be to chr1.1-1000000.ss, chr1.999001-1999000.ss, ...)
2. As in (1), but report unordered sufficient statistics (much more compact and adequate for use with
phyloFit).
msa_split chr1.maf --refseq chr1.fa --in-format MAF --windows 1000000,1000 --out-format SS
--between-blocks 5000 --out-root chr1 --unordered-ss
3. Extract sub-alignments of sites in conserved elements and not in conserved elements, as defined by a
BED file (coordinates assumed to be for 1st sequence). Read multiple alignment in FASTA format.
msa_split mydata.fa --features conserved.bed --by-category --out-root mydata
(Output will be to mydata.background-0.fa and mydata.bed_feature-1.fa [latter has sites of category
number 1, defined by bed file] 3. Extract sub-alignments of sites in each of the three codon positions,
as defined by a GFF file (coordinates assumed to be for 1st sequence). Reverse complement genes on minus
strand.
msa_split chr22.maf --in-format MAF --features chr22.gff --by-category --catmap "NCATS 3 ; CDS
1-3" --do-cats CDS --reverse-compl --out-root chr22 --out-format SS
(Output will be to chr22.cds-1.ss, chr22.cds-2.ss, chr22.cds-3.ss)
4. Split an alignment into pieces corresponding to the genes in a GFF file. Assume genes are defined by
the tag "transcript_id".
msa_split cftr.fa --features cftr.gff --by-group transcript_id
5. Obtain a sub-alignment for each of a set of regulatory regions, as defined in a BED file.
msa_split chr22.maf --in-format MAF --refseq chr22.fa --features chr22.reg.bed --for-features
--out-root chr22.reg
OPTIONS
Splitting options
--windows, -w <win_size,win_overlap>
Split the alignment into "windows" of size <win_size> bases, overlapping by <win_overlap>.
--by-category, -L
(Requires --features) Split by category, as defined by annotations file and (optionally) category
map (see --catmap)
--by-group, -P <tag>
(Requires --features) Split by groups in annotation file, as defined by specified tag. Splits
midway between every pair of consecutive groups. Features will be sorted by group. There should
be no overlapping features (see 'refeature --unique').
--for-features, -F (Requires --features) Extract section of alignment corresponding to every feature.
There will be no output for regions not covered by features.
--by-index, -p <indices> List of explicit indices at which to split alignment (comma-separated). If the
list of indices is "10,20", then sub-alignments will be output for sites 1-9, 10-19, and
20-<msa_len>. Note that the indices are relative to the input alignment, and not necessarily in
genomic coordinates.
--npartitions, -n <number>
Split alignment equally into specified number of partitions.
--between-blocks, -B <radius> (Not for use with --by-category or --for-features) Try to partition at
sites between alignment blocks. Assumes a reference sequence alignment, with the first sequence
as the reference seq (as created by multiz). Blocks of 30 sites with gaps in all sequences but
the reference seq are assumed to indicate boundaries between alignment blocks. Partition indices
will not be moved more than <radius> sites.
--features, -g <fname>
(For use with --by-category, --by-group, --for-features, or --windows) Annotations file. May be
GFF, BED, or genepred format. Coordinates are assumed to be in the coordinate frame of the first
sequence in the alignment (assumed to be the reference sequence).
--catmap, -c <fname>|<string> (Optionally use with --by-category) Mapping of feature types to category
numbers. Can either give a filename or an "inline" description of a simple category map, e.g.,
--catmap "NCATS = 3 ; CDS 1-3" or --catmap "NCATS = 1 ; UTR 1".
--refidx, -d <frame_index>
(For use with --windows or --by-index) Index of frame of reference for split indices. Default is
1 (1st sequence assumed reference).
File names & formats, type of output, etc.
--in-format, -i FASTA|PHYLIP|MPM|MAF|SS Input alignment file format. Default is to guess format from
file contents.
--refseq, -M <fname>
(For use with --in-format MAF) Name of file containing reference sequence, in FASTA format.
--out-format, -o FASTA|PHYLIP|MPM|SS Output alignment file format. Default is FASTA.
--out-root, -r <name> Filename root for output files (default "msa_split").
--sub-features, -f (For use with --features) Output subsets of features corresponding to subalignments.
Features overlapping partition boundaries will be discarded. Not permitted with
--by-category.
--reverse-compl, -s
Reverse complement all segments having at least one feature on the reverse strand and none on the
positive strand. For use with --by-group. Can also be used with --by-category to ensure all
sites in a category are represented in the same strand orientation.
--gap-strip, -G ALL|ANY|<seqno>
Strip columns in output alignments containing all gaps, any gaps, or gaps in the specified
sequence (<seqno>; indexing begins with one). Default is not to strip any columns.
--seqs, -l <seq_list> Include only specified sequences in output. Indicate by
sequence number or name (numbering starts with 1 and is evaluated *after* --order is applied).
--exclude, -x Exclude rather than include specified sequences.
--order, -O <name_list>
Change order of rows in alignment to match sequence names specified in name_list. If a name
appears in name_list but not in the alignment, a row of gaps will be inserted.
--min-informative, -I <n>
Only output alignments having at least <n> informative sites (sites at which at least two non-gap
and non-N gaps are present).
--do-cats, -C <cat_list> (For use with --by-category) Output sub-alignments for only the specified
categories (column-delimited list).
--tuple-size, -T <tuple_size>
(for use with --by-category or --out-format SS) Size of tuples of columns to consider in
downstream analysis (e.g., with context-dependent phylogenetic models; see 'phyloFit'). With
--by-category, insert tuple_size-1 columns of missing data between sites that were not adjacent in
the original alignment, to avoid creating artificial context. With --out-format SS, express
sufficient statistics in terms of tuples of specified size.
--unordered-ss, -z (For use with --out-format SS) Suppress the portion of the sufficient statistics
concerned with the order in which columns appear.
--summary, -S
Output summary of each output alignment to a file with suffix ".sum" (includes base frequencies
and numbers of gapped columns).
Other
--quiet, -q Proceed quietly.
--help, -h
Print this help message.