Provided by: sumtrees_4.4.0-1_all bug

NAME

       sumtrees - Phylogenetic Tree Summarization and Annotation

SYNOPSIS

       sumtrees [-i FORMAT] [-b BURNIN] [--force-rooted] [--force-unrooted]

DESCRIPTION

       SumTrees  is  a  program  to  summarize  non-parameteric  bootstrap  or Bayesian posterior
       probability support for splits or clades on phylogenetic trees.

       The basis of the support  assessment  is  typically  given  by  a  set  of  non-parametric
       bootstrap  replicate tree samples produced by programs such as GARLI or RAxML, or by a set
       of MCMC tree samples produced by programs such as Mr. Bayes or BEAST.  The  proportion  of
       trees out of the samples in which a particular split is found is taken to be the degree of
       support for that split as indicated by the samples. The samples that are the basis of  the
       support  can  be  distributed  across  multiple  files, and a burn-in option allows for an
       initial number of trees in each file to be excluded from the  analysis  if  they  are  not
       considered to be drawn from the true support distribution.

       Summarizations  collections  of  trees,  e.g., MCMC samples from a posterior distribution,
       non-parametric bootstrap replicates, mapping posterior probability, support, or  frequency
       that splits/clades are found in the source set of trees onto a target tree.

OPTIONS

   Source Options:
       TREE-FILEPATH
              Source(s)  of  trees  to  summarize.  At  least  one  valid source of trees must be
              provided. Use '-' to specify reading from standard input (note that  this  requires
              the input file format to be explicitly set using the '--source-format' option).

       -i FORMAT, --input-format FORMAT, --source-format FORMAT
              Format  of  all  input  trees  (defaults to handling either NEXUS or NEWICK through
              inspection; it is more efficient to explicitly specify the format if it is known).

       -b BURNIN, --burnin BURNIN
              Number of trees to skip from the  beginning  of  *each*  tree  file  when  counting
              support (default: 0).

       --force-rooted, --rooted
              Treat source trees as rooted.

       --force-unrooted, --unrooted
              Treat source trees as unrooted.

       -v, --ultrametricity-precision, --branch-length-epsilon
              Precision  to  use  when  validating ultrametricity (default: 1e-05; specify '0' to
              disable validation).

       --weighted-trees
              Use weights of  trees  (as  indicated  by  '[&W  m/n]'  comment  token)  to  weight
              contribution of splits found on each tree to overall split frequencies.

       --preserve-underscores
              Do   not   convert  unprotected  (unquoted)  underscores  to  spaces  when  reading
              NEXUS/NEWICK format trees.

       --taxon-name-filepath FILEPATH
              Path to file listing all the taxon names or labels that will be  found  across  the
              entire  set  of  source  trees. This file should be a plain text file with a single
              name list on each line. This file is only read when multiprocessing ('-M' or  '-m')
              is  requested. When multiprocessing using the '-M' or '-m' options, all taxon names
              need to be defined in advance of any actual tree analysis. By default this is  done
              by  reading the first tree in the first tree source and extracting the taxon names.
              At best, this is, inefficient, as it involves an extraneous reading of the tree. At
              worst,  this  can  be  erroneous,  if the first tree does not contain all the taxa.
              Explicitly providing the taxon names via this option can avoid these issues.

   Target Tree Topology Options:
       -t FILE, --target-tree-filepath FILE
              Summarize support and other information  from  the  source  trees  to  topology  or
              topologies  given  by  the  tree(s)  described  in FILE. If no use-specified target
              topologies are given, then a summary topology will be used as the target.  Use  the
              '-s' or '--summary-target' to specify the type of summary tree to use.

       -s SUMMARY-TYPE, --summary-target SUMMARY-TYPE
              Construct  and summarize support and other information from the source trees to one
              of the following summary topologies: - 'consensus'

       A consensus tree. The minimum frequency
              threshold  of  clades  to  be  included  can  be  specified  using  the   '-f'   or
              '--min-clade-freq'  flags.  This is the DEFAULT if a user- specified target tree is
              not given through the '-t' or '--target-tree-filepath' options.

       - 'mcct'
              The maximum clade credibility tree. The tree from the source set that maximizes the
              *product* of clade posterior probabilities.

       - 'msct'
              The maximum clade credibility tree. The tree from the source set that maximizes the
              *product* of clade posterior probabilities.

   Target Tree Supplemental Options:
       -f #.##, --min-consensus-freq #.##, --min-freq #.##, --min-clade-freq #.##
              If using a  consensus  tree  summarization  strategy,  then  this  is  the  minimum
              frequency  or  probability  for  a clade or a split to be included in the resulting
              tree (default: > 0.5).

       --allow-unknown-target-tree-taxa
              Do not fail with error if target tree(s) have taxa not  previously  encountered  in
              source trees or defined in the taxon discovery file.

   Target Tree Rooting Options:
       --root-target-at-outgroup TAXON-LABEL
              Root target tree(s) using specified taxon as outgroup.

       --root-target-at-midpoint
              Root target tree(s) at midpoint.

       --set-outgroup TAXON-LABEL
              Rotate  the  target trees such the specified taxon is in the outgroup position, but
              do not explicitly change the target tree rooting.

   Target Tree Edge Options:
       -e STRATEGY, --set-edges STRATEGY, --edges STRATEGY
              Set the edge lengths of  the  target  or  summary  trees  based  on  the  specified
              summarization STRATEGY: - 'mean-length'

       Edge lengths will be set to the mean of the
              lengths of the corresponding split or clade in the source trees.

       - 'median-length'
              Edge lengths will be set to the median of the

       lengths of the corresponding split or clade in
              the source trees.

       - 'mean-age'
              Edge  lengths  will be adjusted so that the age of subtended nodes will be equal to
              the mean age of the corresponding split or clade in the source trees. Source  trees
              will need to to be ultrametric for this option.

       - 'median-age'
              Edge  lengths  will be adjusted so that the age of subtended nodes will be equal to
              the median age of the corresponding split or clade  in  the  source  trees.  Source
              trees will need to to be ultrametric for this option.

       - support
              Edge  lengths  will  be  set  to the support value for the split represented by the
              edge.

       - 'keep'
              Do not change the existing edge lengths. This is the DEFAULT if target tree(s)  are
              sourced from an external file using the '-t' or '--targettree-filepath' option

       - 'clear'
              Edge lengths will be cleared from the target trees if they are present.

       Note the default settings varies according to the
              following, in order of preference: (1) If target trees are specified using the '-t'
              or

       '--target-tree-filepath' option, then the default edge
              summarization strategy is: 'keep'.

       (2) If target trees are not specified, but the
              '--summarize-node-ages' option is specified, then the  default  edge  summarization
              strategy is: 'mean-age'.

       (3) If no target trees are specified and the
              node  ages  are NOT specified to be summarized, then the default edge summarization
              strategy is: 'mean-length'.

       --force-minimum-edge-length FORCE_MINIMUM_EDGE_LENGTH
              (If setting edge lengths) force all edges to be at least this length.

       --collapse-negative-edges
              (If setting edge lengths) force parent node ages to be  at  least  as  old  as  its
              oldest child when summarizing node ages.

   Target Tree Annotation Options:
       --summarize-node-ages, --ultrametric, --node-ages
              Assume  that  source  trees  are ultrametic and summarize node ages (distances from
              tips).

       -l {support,keep,clear}, --labels {support,keep,clear}
              Set the node labels of the summary or target tree(s): - 'support'

       Node labels will be set to the support value for
              the clade represented by the node. This is the DEFAULT.

       - 'keep'
              Do not change the existing node labels.

       - 'clear'
              Node labels will be cleared from the target trees if they are present.

       --suppress-annotations, --no-annotations
              Do NOT annotate nodes and edges with any summarization  information  metadata  such
              as.support values, edge length and/or node age summary statistcs, etc.

   Support Expression Options:
       -p, --percentages
              Indicate  branch  support  as percentages (otherwise, will report as proportions by
              default).

       -d #, --decimals #
              Number of decimal places in indication of support values (default: 8).

   Output Options:
       -o FILEPATH, --output-tree-filepath FILEPATH, --output FILEPATH
              Path to output file (if not specified, will print to standard output).

       -F {nexus,newick,phylip,nexml}, --output-tree-format {nexus,newick,phylip,nexml}
              Format of the output tree file (if not specified, defaults to input format, if this
              has been explicitly specified, or 'nexus' otherwise).

       -x PREFIX, --extended-output PREFIX
              If  specified,  extended summarization information will be generated, consisting of
              the following files: - '<PREFIX>.topologies.trees'

       A collection of topologies found in the sources
              reported with their associated posterior probabilities as metadata annotations.

       - '<PREFIX>.bipartitions.trees'
              A  collection  of  bipartitions,  each  represented  as  a  tree,  with  associated
              information as metadataannotations.

       - '<PREFIX>.bipartitions.tsv'
              Table  listing  bipartitions  as a group pattern as the key column, and information
              regarding each the bipartitions as the remaining columns.

       - '<PREFIX>.edge-lengths.tsv'
              List of bipartitions and corresponding edge lengths. Only generated if edge lengths
              are summarized.

       - '<PREFIX>.node-ages.tsv'
              List  of  bipartitions  and  corresponding  ages.   Only generated if node ages are
              summarized.

       --no-taxa-block
              When writing NEXUS format output, do  not  include  a  taxa  block  in  the  output
              treefile (otherwise will create taxa block by default).

       --no-analysis-metainformation, --no-meta-comments
              Do  not  include  meta-information  describing  the  summarization  parameters  and
              execution details.

       -c ADDITIONAL_COMMENTS, --additional-comments ADDITIONAL_COMMENTS
              Additional comments to be added to the summary file.

       -r, --replace
              Replace/overwrite output file without asking if it already exists.

   Parallel Processing Options:
       -M, --maximum-multiprocessing
              Run in parallel mode using as many processors as available, up  to  the  number  of
              sources.

       -m NUM-PROCESSES, --multiprocessing NUM-PROCESSES
              Run  in  parallel mode with up to a maximum of NUMPROCESSES processes ('max' or '#'
              means to run in as many processes as there are cores on the  local  machine;  i.e.,
              same as specifying '-M' or '--maximummultiprocessing').

   Program Logging Options:
       -g LOG-FREQUENCY, --log-frequency LOG-FREQUENCY
              Tree processing progress logging frequency (default: 500; set to 0 to suppress).

       -q, --quiet
              Suppress ALL logging, progress and feedback messages.

   Program Error Options:
       --ignore-missing-support
              Ignore missing support tree files (note that at least one must exist).

   Program Information Options:
       -h, --help
              Show help information for program and exit.

       --citation
              Show citation information for program and exit.

       --usage-examples
              Show usage examples of program and exit.

       --describe
              Show information regarding your DendroPy and Python installations and exit.

AUTHORS

       Jeet Sukumaran and Mark T. Holder

SEE ALSO

       If any stage of your work or analyses relies on code or programs from this library, either
       directly or  indirectly  (e.g.,  through  usage  of  your  own  or  third-party  programs,
       pipelines,  or  toolkits  which  use,  rely  on,  incorporate,  or are otherwise primarily
       derivative of code/programs in this library), please cite:

              Sukumaran, J and MT Holder. 2010.  DendroPy:  a  Python  library  for  phylogenetic
              computing. Bioinformatics 26: 1569-1571.

              Sukumaran,  J and MT Holder. SumTrees: Phylogenetic Tree Summarization.  4.0.0 (Jan
              31 2015). Available at https://github.com/jeetsukumaran/DendroPy.

       Note that, in the interests of scientific reproducibility, you should describe in the text
       of  your  publications not only the specific version of the SumTrees program, but also the
       DendroPy library used in your analysis. For your information,  you  are  running  DendroPy
       4.0.2.