SUMAC (Supermatrix Constructor) is a Python package to data-mine GenBank, construct phylogenetic supermatrices, and assess the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. SUMAC calculates a novel metric, Missing Sequence Decisiveness Scores (MSDS), which measure how much each individual missing sequence contributes to the decisiveness of the matrix. MSDS can be used to compare supermatrices and prioritize the acquisition of new sequence data.
SUMAC is designed to be run as a command-line program, though the modules can also be imported and used in other Python scripts. SUMAC will assemble supermatrices for any taxonomic group recognized in GenBank, and is optimized to run on multicore systems by utilizing multiple parallel processes. Please see the SUMAC user manual for many more details.
SUMAC works on OSX and Linux. Windows is not currently supported.
❗ USEARCH bug 9.15 will cause USEARCH to crash during a SUMAC run. This bug affects USEARCH versions v9.2.64 and v9.0.2132. Please ensure you use a different version of USEARCH with SUMAC. Until a new version is released use v8.1 which you can download here.
- SUMAC v2.23 now allows multiple guide sequences for each target locus.
- SUMAC v2.22 updates SUMAC to handle SeqRecord comparisons deprecated in Biopython 1.67.
- SUMAC v2.21 handles a bug in Biopython's GenBank parsing that could cause SUMAC to crash.
- SUMAC v2.2 allows multiple taxonomic groups to be searched for (not just a single ingroup and outgroup). See manual for details.
- SUMAC v2.1 greatly improves the handling of taxonomic names, adds the
--min_clustersflag to set the minimum number of taxa to include in a cluster, and other additional error checks. - SUMAC v2.0 is significantly faster than previous versions due to a new clustering algorithm.
Freyman, W.A. 2015. SUMAC: constructing phylogenetic supermatrices and assessing partially decisive taxon coverage. Evolutionary Bioinformatics 2015:11 263-266
Copyright 2016 Will Freyman - freyman@berkeley.edu
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
Python 2.7
Biopython
MAFFT v6.9+
USEARCH
BLAST+ (optional)
The quick way:
sudo pip install sumac
For more detailed instructions see the SUMAC user manual
python -m sumac [-h] [--download_gb DOWNLOAD_GB]
[--download_gb2 DOWNLOAD_GB2] [--path PATH]
[--ingroup INGROUP] [--outgroup OUTGROUP] [--cores CORES]
[--id ID] [--evalue EVALUE] [--length LENGTH]
[--maxlength MAXLENGTH] [--minlength MINLENGTH]
[--min_clusters MIN_CLUSTERS] [--max_ingroup MAX_INGROUP] [--guide GUIDE]
[--alignments ALIGNMENTS [ALIGNMENTS ...]]
[--salignments SALIGNMENTS [SALIGNMENTS ...]] [--search]
[--decisiveness] [--hac] [--slink]
-h, --help show this help message and exit [8/1029]
--download_gb DOWNLOAD_GB, -d DOWNLOAD_GB
Name of the GenBank division to download (e.g. PLN or
MAM).
--download_gb2 DOWNLOAD_GB2, -d2 DOWNLOAD_GB2
Name of the optional second GenBank division to
download. Use this option if the ingroup and outgroup
are in different GenBank divisions.
--path PATH, -p PATH Absolute path to download GenBank files to. Defaults
to ./genbank/
--ingroup INGROUP, -i INGROUP
Ingroup clade to build supermatrix.
--outgroup OUTGROUP, -o OUTGROUP
Outgroup clade to build supermatrix.
--cores CORES, -c CORES
The number of CPU cores to use for parallel
processing. Defaults to the max available.
--id ID, -id ID UCLUST id threshold to cluster taxa. Defaults to 0.50
--evalue EVALUE, -e EVALUE
BLAST E-value threshold to cluster taxa. Defaults to
1e-10
--length LENGTH, -l LENGTH
Threshold of sequence length percent similarity to
cluster taxa. Defaults to 0.25
--maxlength MAXLENGTH, -maxl MAXLENGTH
Maximum length of sequences to include in UCLUST
clusters. Defaults to 5000
--minlength MINLENGTH, -minl MINLENGTH
Minimum length of sequences to include in UCLUST
clusters. Defaults to 100
--min_clusters MIN_CLUSTERS, -minc MIN_CLUSTERS
Minimum number of taxa needed for clusters. Defaults
to 4
--max_ingroup MAX_INGROUP, -m MAX_INGROUP
Maximum number of taxa to include in ingroup. Default
is none (no maximum limit).
--guide GUIDE, -g GUIDE
FASTA file containing sequences to guide cluster
construction. If this option is selected then all-by-
all BLAST comparisons are not performed.
--alignments ALIGNMENTS [ALIGNMENTS ...], -a ALIGNMENTS [ALIGNMENTS ...]
List of aligned FASTA files to build supermatrix
instead of mining GenBank.
--salignments SALIGNMENTS [SALIGNMENTS ...], -sa SALIGNMENTS [SALIGNMENTS ...]
List of SUMAC alignments to build supermatrix instead
of mining GenBank.
--search, -s Turn on search and cluster mode. Will not make
alignments or supermatrix.
--decisiveness, -de Calculate partial decisiveness. For larger matrices
this may be slow.
--hac Use HAC single-linkage clustering algorithm instead of
the default UCLUST algorithm.
--slink Use the SLINK clustering algorithm instead of the
default UCLUST algorithm.