GCtree specifications

Information


Unique identifier OMICS_29148
Name GCtree
Alternative name Genotype-Collapsed tree
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A sequence for each observed individual/cell, and an additional sequence containing the ancestral genotype of all observed sequences.
Input format FASTA,PHYLIP
Output data A text file mapping collapsed sequenced ids to cell ids from the original input file, one with ids to their abundances, a phylip alignment file of collapsed sequences for computing parsimony trees, a directory of parsimony tree output from PHYLIP's dnapars, a rendered tree images for each of the parsimony trees, an histogram of genotype abundances, a rank plot of GCtree likelihoods for the parsimony trees, a log file containing parameter fits, numerical likelihood results, and any other program messages, and a python pickle file containing the parsimony trees.
Output format PDF+SVG
Operating system Unix/Linux, Mac OS
Programming languages Perl, Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements scons, scipy, matplotlib, seaborn, pandas, biopython, ete3, nestly, PHYLIP, X11 or xvfb-run, seqmagick
Maintained Yes

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Maintainers


  • person_outline Frederick A. Matsen <>
  • person_outline Vladimir Minin <>

Publication for Genotype-Collapsed tree

GCtree institution(s)
Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA; Department of Statistics, University of California, Irvine, CA, USA
GCtree funding source(s)
Supported in part by a National Institutes of Health National Human Genome Research Institute Genome Training Grant (5T32HG000035-23), National Institutes of Health grant R01 AI119006, National Institutes of Health grant R01 GM113246 and National Science Foundation grants CISE-1564137 and CISE1561334, in part by a Faculty Scholar grant from the Howard Hughes Medical Institute and the Simons Foundation, as well as by National Institutes of Health grant R01 AI120961 (PI Overbaugh).

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