SPIDIR specifications


Unique identifier OMICS_16629
Alternative name Species Informed Distance-based Reconstruction
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.9
Stability Stable
Source code URL http://compbio.mit.edu/spidir/pub/software/spidir-0.9.tar.gz
Maintained Yes


No version available


  • person_outline Manolis Kellis

Publication for Species Informed Distance-based Reconstruction

SPIDIR citation


GIGA: a simple, efficient algorithm for gene tree inference in the genomic age

BMC Bioinformatics
PMCID: 2905364
PMID: 20534164
DOI: 10.1186/1471-2105-11-312

[…] ecies tree. The soft parsimony algorithm [] extends tree reconciliation to minimize duplications and losses given an uncertain species tree (containing "soft" polytomies or multifurcating nodes). The SPIDIR algorithm [] extends the sequence evolution paradigm by learning lineage-specific rate parameters for phylogenetic reconstruction over a large number of orthologous gene trees simultaneously. T […]

SPIDIR institution(s)
MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
SPIDIR funding source(s)
This work was funded by the Ruth L. Kirschstein National Research Service Award (NRSA).

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