phybin - Online in the Cloud

PROGRAM:

NAME

phybin - binning/clustering newick trees by topology

SYNOPSIS

phybin [OPTION...] files or directories...

DESCRIPTION

PhyBin takes Newick tree files as input. Paths of Newick files can be passed directly on
the command line. Or, if directories are provided, all files in those directories will be
read. Taxa are named based on the files containing them. If a file contains multiple
trees, all are read by phybin, and the taxa name then includes a suffix indicating the
position in the file:

e.g. FILENAME_0, FILENAME_1, etc.

When clustering trees, Phybin computes a complete all-to-all Robinson-Foulds distance
matrix. If a threshold distance (tree edit distance) is given, then a flat set of
clusters will be produced in files clusterXX_YY.tr. Otherwise it produces a full
dendogram.

Binning mode provides an especially quick-and-dirty form of clustering. When running with
the --bin option, only exactly equal trees are put in the same cluster. Tree
pre-processing still applies, however: for example collapsing short branches.

USAGE NOTES:
* Currently phybin ignores input trees with the wrong number of taxa.

* If given a directory as input phybin will assume all contained files are Newick trees.

OPTIONS

-v --verbose
print WARNINGS and other information (recommended at first)

-V --version
show version number

-o DIR --output=DIR
set directory to contain all output files (default "./phybin_out/")

--selftest
run internal unit tests

Clustering Options
--bin Use simple binning, the cheapest form of 'clustering'

--single
Use single-linkage clustering (nearest neighbor)

--complete
Use complete-linkage clustering (furthest neighbor)

--UPGMA
Use Unweighted Pair Group Method (average linkage) - DEFAULT mode

--editdist=DIST
Combine all clusters separated by DIST or less. Report a flat list of clusters.
Irrespective of whether this is activated, a hierarchical clustering
(dendogram.pdf) is produced.

Select Robinson-Foulds (symmetric difference) distance algorithm:
--hashrf
(default) use a variant of the HashRF algorithm for the distance matrix

--tolerant
use a slower, modified RF metric that tolerates missing taxa

Visualization
-g --graphbins
use graphviz to produce .dot and .pdf output files

-d --drawbins
like -g, but open GUI windows to show each bin's tree

-w --view
for convenience, "view mode" simply displays input Newick files without binning

--showtrees
Print (textual) tree topology inside the nodes of the dendrogram

--highlight=FILE
Highlight nodes in the tree-of-trees (dendrogram) consistent with the. given tree
file. Multiple highlights are permitted and use different colors.

--interior
Show the consensus trees for interior nodes in the dendogram, rather than just
points.

Tree pre-processing
--prune=TAXA
Prune trees to only TAXA before doing anything else. Space and comma separated
lists of taxa are allowed. Use quotes.

-b LEN --minbranchlen=LEN
collapse branches less than LEN

--minbootstrap=INT
collapse branches with bootstrap values less than INT

Extracting taxa names
-p NUM --nameprefix=NUM
Leaf names in the input Newick trees can be gene names, not taxa. Then it is
typical to extract taxa names from genes. This option extracts a prefix of NUM
characters to serve as the taxa name.

-s STR --namesep=STR
An alternative to --nameprefix, STR provides a set of delimeter characters, for
example '-' or '0123456789'. The taxa name is then a variable-length prefix of
each gene name up to but not including any character in STR.

-m FILE --namemap=FILE
Even once prefixes are extracted it may be necessary to use a lookup table to
compute taxa names, e.g. if multiple genes/plasmids map onto one taxa. This option
specifies a text file with find/replace entries of the form "<string> <taxaname>",
which are applied AFTER -s and -p.

Utility Modes
--rfdist
print a Robinson Foulds distance matrix for the input trees

--setdiff
for convenience, print the set difference between cluster*.txt files

--print
simply print out a concise form of each input tree

--printnorms
simply print out a concise and NORMALIZED form of each input tree

--consensus
print a strict consensus tree for the inputs, then exit

--matching
print a list of tree names that match any --highlight argument

Use phybin online using onworks.net services