ProbCons specifications

Information


Unique identifier OMICS_00986
Name ProbCons
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/ProbCons

Documentation


Maintainers


  • person_outline Chuong Do <>
  • person_outline Mahathi Mahabhashyam <>

Information


Unique identifier OMICS_00986
Name ProbCons
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.12
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Chuong Do <>
  • person_outline Mahathi Mahabhashyam <>

ProbCons article

ProbCons citations

 (4)
2015
PMCID: 4408586

[…] probabilities of sites being under positive selection in the m8 and branch-site models we used the bayes empirical bayes (beb) approach implemented in paml [86]., we repeated the analyses using probcons [87] for aligning sequences. however, we only report the results from alignments produced by prographmsa, as these alignments give more conservative estimates and hence a smaller chance […]

2012
PMCID: 3318445

[…] and we wanted to examine only annotated protein-coding genes., the amino acid sequences corresponding to the resulting 5,282 gene sets of size n ≥ 4 were extracted from genbank and aligned using probcons (do et al. 2005). ambiguously aligned regions of the alignments were removed using gblocks version 0.91b (castresana 2000) with parameter settings as follows: minimum number of sequences […]

2011
PMCID: 3212841

[…] gene sets if one or the other term is not required by context., the amino acid sequences corresponding to the 5282 protein sets (families) of size n ≥ 4 were extracted from genbank and aligned using probcons [46] with default parameter settings. following alignment, ambiguously aligned regions of the alignments were removed using gblocks version 0.91b [47] with the following parameter settings: […]

2009
PMCID: 2607023

[…] it reports for every pair of positions in the two sequences, the posterior probability that they are aligned. morph was run to produce such a probabilistic alignment of every pair of species. probcons takes such pair-wise alignment probabilities and builds a multiple sequence alignment progressively, while using the “consistency transformation”: the probability of alignment of two […]

ProbCons institution(s)
Department of Computer Science, Stanford University, Stanford, CA, USA
ProbCons funding source(s)
Supported by an NSF Graduate Fellowship.

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