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NAME

       msa_view - Provides various kinds of "views" of one or more multiple

DESCRIPTION

       Provides  various  kinds  of  "views"  of  one or more multiple alignments.  Can extract a
       sub-alignment from an alignment (by row or by column) or combine several  alignments  into
       one.   Also  can  extract  the  sufficient  statistics  for  phylogenetic analysis from an
       alignment, optionally accounting for site categories that  are  defined  by  an  auxiliary
       annotations  file.   Supports  various  other  functions,  including gap stripping, column
       randomization, and reordering of sequences.  Capable of  reading  and  writing  in  a  few
       common  formats.   Can be used for file conversion (by default, output is the entire input
       alignment).

EXAMPLE

       (See below for more details on options)

       1. Convert alignment formats (default input and output is FASTA)

              msa_view myfile.fa --out-format PHYLIP > myfile.ph

              msa_view myfile2.raw --in-format MPM > myfile2.fa

       2. Obtain a sub-alignment by position, using the coordinate frame of the first sequence in
       the alignment.

              msa_view myfile.fa --start 1234 --end 5678 --refidx 1 > mysub.fa

       3. Obtain a sub-alignment by sequence.

              msa_view myfile.fa --seqs 1,4,5 > seqs145.fa

              msa_view myfile.fa --seqs 1,4,5 --exclude > seqs236.fa

       (can also specify sequences by name, e.g., --seqs cow,rat,pig)

       4. Concatenate alignments.

              msa_view --aggregate human,mouse,rat myf1.fa myf2.fa myf3.fa > concat.fa

       (source  alignments may have different subsets of sequences and may use different sequence
       orders; here, human,mouse,rat defines full set and order in output alignment)

       5. Extract sufficient statistics from a FASTA file.

              msa_view myfile.fa --out-format SS > myfile.ss

       6. Extract sufficient statistics from a MAF file for a complete human chromosome.  (Can be
       used by phyloFit.)

              msa_view chr1.maf --out-format SS > chr1.ss

       7.  As in (6), but include information about regions of the reference sequence not present
       in the MAF file, and include a representation of the  order  in  which  alignment  columns
       occur (needed by programs such as phastCons or exoniphy).

              msa_view chr1.maf --refseq chr1.fa --out-format SS > chr1.ordered.ss

       8.  As in (6), but collect statistics for pairs of adjacent sites (can be used by phyloFit
       to estimate a dinucleotide model).

              msa_view chr1.maf --out-format SS --tuple-size 2 > chr1.pairs.ss

       9. Pool sufficient statistics from several human chromosomes.

              msa_view --aggregate human,mouse,rat --out-format  SS  chr1.ss  chr2.ss  chr3.ss  >
              chr123.ss

       10.  Extract  separate  sufficient statistics for the three codon positions, as defined by
       annotations in a GFF file.

              msa_view chr1.maf --features chr22.gff --catmap "NCATS = 3; CDS  1-3"  --out-format
              SS > chr22.pos.ss

       11.  As  in  (10), but re-orient genes on - strand so that stats reflect + strand.  Assume
       genes are defined by tag "transcript_id".

              msa_view  chr1.maf  --features  chr22.gff   --catmap   "NCATS   =   3;   CDS   1-3"
              --reverse-groups transcript_id --out-format SS > chr22.pos.ss

OPTIONS

   Obtaining sub-alignments and combining alignments
       --start, -s <start_col>

              Starting  column  of  sub-alignment  (indexing starts with 1).  Default is 1.  Note
              that coordinates use the frame of reference of the entire alignment unless --refidx
              1 is specified.

       --end, -e <end_col>

       Ending column of sub-alignment.
              Default is length of

       alignment.
              Note that coordinates use the frame of reference

              of the entire alignment unless --refidx 1 is specified.

       --seqs,  -l  <seq_list> Comma-separated list of sequences to include (default) exclude (if
              --exclude).  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.

       --refidx, -r <ref_seq>

       Index of reference sequence for coordinates.
              Use 0 to

              indicate the coordinate system of the alignment as a whole (this is the default).

       --aggregate, -A <name_list>

              (Not  compatible with --start or --end) Create an aggregate alignment from a set of
              alignment files, by concatenating individual alignments.  If used with --out-format
              SS  and  --unordered-ss,  the  aggregate alignment will never be created explicitly
              (recommended for large data sets).  The argument <name_list>  must  be  a  list  of
              sequence  names, including all names in all specified alignments (missing sequences
              will be replaced by rows of  missing  data).   The  standard  <msa_fname>  argument
              should be replaced with a list of (whitespaceseparated) file names.

       --split-all, -X <filename root>

              Split  output  alignment  into  separate  fasta  files  by  species.   File  naming
              convention is filename_root.species.fa. If used with  --gap-strip,  gap  characters
              will be stripped from all output files.  In this case, '--gap-strip <s>' should NOT
              be used (ALL or ANY should both work fine).

   File formats, gap stripping, reordering, etc.
       --in-format, -i PHYLIP|FASTA|MPM|MAF|SS

       (Default is to guess format from file contents).
              Input file

       format.
              FASTA is as usual.  PHYLIP is compatible with the formats

       used in the PHYLIP and PAML packages.
              MPM is the format used by the

              MultiPipMaker aligner and some other of Webb Miller's older tools.  MAF  ("Multiple
              Alignment  Format")  is  used  by  MULTIZ/TBA and the UCSC Genome Browser.  SS is a
              simple format describing  the  sufficient  statistics  for  phylogenetic  inference
              (distinct  columns or tuple of columns and their counts).  Use --out-format SS with
              --in-format MAF for best efficiency (explicit alignment is never  created).   Also,
              use --unordered-ss if possible.

       --out-format, -o PHYLIP|FASTA|MPM|SS (Default FASTA) Output file format.

       --alphabet, -a <alphabet_string>

       Use the specified alphabet (default "ACGT").
              In addition,

              '-'  characters are assumed to represent alignment gaps, and '*' and 'N' characters
              are allowed for missing data.  Alphabetical letters not in  the  alphabet  will  be
              converted  to  'N's  upon  input.   This  option is ignored with SS input (alphabet
              specified within SS files.)

       --soft-masked, -f

              Implies --alphabet 'ACGTNacgtn', useful for soft-masked sequences.

       --unmask, -u

              Remove soft-masking; convert to uppercase.

       --pretty,  -P  Pretty-print  alignment  (use  '.'  when  character  matches  corresponding
              character in first sequence).  Ignored if --out-format SS is selected.

       --gap-strip,  -G  ALL|ANY|<s> Strip columns containing all gaps, any gaps, or a gap in the
              specified sequence (<s>).  Indexing starts at one and refers to  the  list  *after*
              any sequences have been added or subtracted (via --seqs and --exclude or --order).

       --collapse-missing, -p

              (For  use  with  -o  SS)  Convert  all  missing-data  characters  and  gaps  to "*"
              characters.  Can be used to make sufficient  statistics  more  compact,  which  can
              improve  the  performance  of  phyloFit  (all  missing  data and gap characters are
              typically treated the same by phyloFit anyway).

       --mark-missing, -K <maxlen> Convert all gaps  of  length  greater  than  <maxlen>  to  "*"
              characters.   If  --refidx  is  specified  (with  a  positive  index),  gaps in the
              designated reference sequence will not be altered.  This is a useful heuristic  for
              distinguishing  between  microindels  and  regions  of  missing  data (e.g., due to
              large-scale indels, incomplete assemblies, or highly diverged sequences).

       --missing-as-indels, -m

              Convert all missing data characters (Ns and *s) to gap characters, except for Ns in
              a  reference  sequence  specified  by  --refidx, which will be replaced by randomly
              selected nucleotides.  (This allows the coordinate frame for the reference sequence
              to  be  maintained;  this  option  is  only  recommended  if such Ns are rare.)  If
              --refidx is not used, all Ns will be  replaced  by  gaps.   You  may  want  to  use
              --gap-strip ALL with this option.

       --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.  This option is applied to the alignment *before*
              --seqs, --refidx, and --gap-strip are applied.

       --reverse-complement, -V

              Reverse complement output alignment.

       --randomize, -R Randomly permute the columns of the source alignment (done *before* taking
              sub-alignment).  Requires an ordered representation of the alignment (careful using
              with --in-format SS|MAF -- will create full alignment from sufficient statistics).

       --fill-Ns, -N <s:b-e>

              Fill sequence no. <s> with Ns, from <b> to  <e>.  Applied  before  --start,  --end,
              --seqs, --gap-strip, but after --order.  Coordinate frame depends on --refidx.  Can
              be used multiple times.

       --summary-only  -S  Report  only  summary  statistics,  rather  than  complete  alignment.
              Statistics  are  for  alignment  that  would otherwise be output (i.e., after other
              options have been applied).

       --window-summary, -w <win_size> Like -S, but output summary statistics for non-overlapping
              windows of the specified size.  (Sufficient statistics)

       --tuple-size,  -T  <tup_size>  (For  use with --out-format SS).  Represent an alignment in
              terms of tuples of columns of the designated size.  Useful

              with context-dependent phylogenetic models.

       --unordered-ss, -z

       (For use with --out-format SS).
              Suppress the portion of the

              sufficient statistics concerned with the order in which columns appear.  Useful for
              analyses for which order is unimportant.  (MAF input)

       --refseq, -M <fname>

              Read  the  complete  text of the reference sequence from <fname> (FASTA format) and
              combine it with the contents of  the  MAF  file  to  produce  a  complete,  ordered
              representation  of  the  alignment (unaligned regions will be represented by gaps).
              Best used with --out-format SS.  The reference sequence of the MAF file is  assumed
              to be the one that appears first in each block.

       --keep-overlapping, -k

              Keep  blocks  in  MAF  that  have  overlapping  coordinates  in the reference (1st)
              sequence (by default, only the first one is kept).  Useful in extracting  unordered
              stats  from a jumbled collection of MAF blocks (e.g., output of Jim Kent's mafFrags
              program).  Cannot be used with --refseq, --features, or

       --cats-cycle.  (Site categories: all options require --out-format SS)

       --features, -g <gff_fname>

              (Requires --catmap) Read sequence annotations from the  specified  file  (GFF)  and
              label  the  columns  of  the  alignment  accordingly.   Note: UCSC BED and genepred
              formats are now recognized as well.

       --catmap, -c <fname>|<string>

              (optionally use with --features) 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".

       --cats-cycle, -Y  <cycle_size>  (alternative  to  --features  and  --catmap)  Assign  site
              categories  in  cycles  of  the  specified  size,  e.g.,  as  1,2,3,...,1,2,3  (for
              cycle_size == 3).  Useful for in-frame coding sequence, or to partition a data  set
              into nonoverlapping tuples of columns (use with --do-cats).

       --do-cats, -C <cat_list>

       (For use with --features or --cats-cycle)
              Obtain

              sufficient  statistics  only for the specified categories (comma-delimited list, by
              number).

       --codons, -D Extract sufficient statistics for in-frame codons.   Implies  --tuple-size  3
              --cats-cycle 3 --do-cats 3.  Not appropriate

              for use with --features/--catmap.

       --reverse-groups, -W <tag>

              (For  use  with  --features)  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).
              Useful when extracting sufficient statistics for  strand-specific  site  categories
              (e.g., codon positions).

       --4d, -4

              (For  use with --features; assumes coding regions have feature type 'CDS')  Extract
              sufficient  statistics  for  fourfold   degenerate   synonymous   sites.    Implies
              --out-format SS --unordered-stats --tuple-size 3 --reverse-groups transcript_id.

Alignment cleaning

       --clean-coding, -L <seqname>

              Clean  an alignment of coding sequences with respect to a named reference sequence.
              Removes sites with gaps and blocks of gapless  sites  smaller  than  10  codons  in
              length,  ensures  everything is in-frame wrt reference sequence, prohibits in-frame
              stop codons.  Reference sequence must begin with a start codon and end with a  stop
              codon.

       --clean-indels, -I <nseqs>

       Clean an alignment with special attention to indels.
              Sites

              with  fewer  than  <nseqs>  bases  are removed; bases adjacent to indels, and short
              gapless subsequences, are replaced  with  Ns.   If  used  with  --tuple-size,  then
              <tup_size>-1  columns  of  Ns  will be retained between columns not adjacent in the
              original alignment.  Frame is not considered.

   Other
       --help, -h Print this help message.