Provided by: sumtrees_4.4.0-2_all 
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.