sumtrees - Online in the Cloud

PROGRAM:

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 errorneous, 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

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