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SPIMAP specifications


Unique identifier OMICS_14972
Alternative name Species Informed Maximum A Posteriori Gene Tree Reconstruction
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data The gene sequences, the species tree.
Output data The gene tree reconciled to the known species tree, the inferred orthologs, paralogs, gene duplications and loss events.
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.1
Stability Stable
C++ compiler, GNU Scientific, Python
Source code URL http://compbio.mit.edu/spimap/pub/spimap-1.1.tar.gz
Maintained Yes




No version available


  • person_outline Matthew Rasmussen

Publication for Species Informed Maximum A Posteriori Gene Tree Reconstruction

SPIMAP citations


GATC: a genetic algorithm for gene tree construction under the Duplication Transfer Loss model of evolution

BMC Genomics
PMCID: 5954287
PMID: 29764363
DOI: 10.1186/s12864-018-4455-x

[…] methods for gene tree reconstruction assume a simplified model of gene family evolution where gene gain events are reduced to gene duplication (e.g. TreeBeST [], TreeFix [], ProfileNJ [], NOTUNG [], SPIMAP [], Giga []). In fact, the MPR problem for the Duplication-Loss (hereafter denoted DL) model of gene family evolution is linear-time solvable []. By introducing horizontal gene transfer (HGT) e […]


Improved orthologous databases to ease protozoan targets inference

PMCID: 4587786
PMID: 26416523
DOI: 10.1186/s13071-015-1090-0

[…] al best hits, such as OrthoSearch [], OrthoMCL [] and InParanoid []; (ii) that which rely on evolutionary distance calculus, as RSD [, ]; (iii) and that based on phylogenetic trees reconstruction, as SPIMAP [].Many orthologous databases (OD) are created by homology inference methods. This is the case for OrthoMCLDB []; InParanoid []; Roundup []; COG/KOG [] and EggNOG [, ].OrthoSearch [] is a scien […]


Improved gene tree error correction in the presence of horizontal gene transfer

PMCID: 4393519
PMID: 25481006
DOI: 10.1093/bioinformatics/btu806

[…] tion model that makes it possible to extract topological information from the species tree and use it to guide gene tree inference. Some of these methods, such as TreeBest (), PrIME-GSR (DLRS) () and SPIMAP (), reconstruct a gene tree directly from sequence data, but most, such as NOTUNG (), tt (), TreeFix (), AnGST () and MowgliNNI (), take in previously reconstructed gene trees and error-correct […]


The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: A Simulation Study

PLoS One
PMCID: 3581572
PMID: 23451112
DOI: 10.1371/journal.pone.0056925

[…] s groups as output, we created the set of induced orthologous pairs by pairing each member of a group with all other members of that group belonging to a different species. For the tree-based method (SPIMAP) we took the Cartesian product of the two children leafsets of all speciation nodes in the reconciled tree. We then compared the set of predicted pairwise orthologs to the set of true orthologs […]


Evolution at the Subgene Level: Domain Rearrangements in the Drosophila Phylogeny

Mol Biol Evol
PMCID: 3258039
PMID: 21900599
DOI: 10.1093/molbev/msr222

[…] Most methods within our phylogenomic pipeline (e.g., residue correlation matrix, OrthoMCL, SPIMAP) have been evaluated in their respective works (, , ). To evaluate the last step in this pipeline, our architecture scenario reconstruction algorithm STAR-MP, we simulated module evolution, whe […]


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SPIMAP institution(s)
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
SPIMAP funding source(s)
This work was supported by National Science Foundation (NSF) CAREER award NSF 0644282.

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