Provided by: phast_1.5+dfsg-1_amd64 bug


       msa_split - Partitions a multiple sequence alignment either at designated


       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.


       (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,, ...)

       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,,

       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

              msa_split  chr22.maf  --in-format  MAF  --refseq  chr22.fa --features chr22.reg.bed
              --for-features --out-root chr22.reg


   Splitting options
       --windows, -w <win_size,win_overlap>

              Split the alignment  into  "windows"  of  size  <win_size>  bases,  overlapping  by

       --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

       --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

       --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


       --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

       --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

       --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).

       --quiet, -q Proceed quietly.

       --help, -h

              Print this help message.