ProbCons pipeline

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 <>

Publication for ProbCons

ProbCons IN pipelines

 (10)
2018
PMCID: 5794259
PMID: 29388911
DOI: 10.7554/eLife.31529.023

[…] representing the diversity of nrdb were selected by clustering all nrdb sequences from refseq at an identity threshold of 70% using vsearch (rognes et al., 2016). sequences were aligned with probcons (do et al., 2005) and reliable positions for phylogenetic reconstruction were manually selected. a maximum likelihood phylogeny was estimated with fasttree 2 (price et al., 2010)., […]

2017
PMCID: 5570066
PMID: 28854629
DOI: 10.1093/gbe/evx117

[…] the accuracy of this approach has been demonstrated (wolf and koonin 2012; dalquen and dessimoz 2013)., for each pair of orthologous genes, the encoded protein sequences were aligned using probcons, version 1.12 (do et al. 2005), and the resulting alignment was used to align the corresponding cds sequences. for each of the resulting alignments, we estimated the nonsynonymous […]

2017
PMCID: 5633207
PMID: 28953979
DOI: 10.1371/journal.ppat.1006589

[…] paracoccidioides brasiliensis pb03 (gca_000150475.2) and pb18 (gca_000150735.2); and emmonsia crescens uamh 3008 (gca_001008285.1). the inferred protein sequences were aligned with probcons [63], and alignments were formatted with jalview [64]., four-day hc cultures were collected and yeast were pelleted by centrifugation. the supernatants were sterile-filtered through 0.22μm […]

2017
PMCID: 5823240
PMID: 28992183
DOI: 10.1093/jmcb/mjx024

[…] factor receptor domain’, ‘kazal-type serine protease inhibitor’, ‘trypsin-like serine protease’, and ‘pdz domain-like’ families, respectively., a multiple sequence alignment was generated using probcons (do et al., 2005). this was used with mrbayes (ronquist et al., 2012) to generate a phylogenetic tree, using a mixed amino acid model and a 4-category gamma distribution with invariant […]

2015
PMCID: 4373515
PMID: 25881070
DOI: 10.1186/s12879-015-0870-7

[…] those of a. calcoaceticus xm1570 to generate core conserved proteins, which were defined with a minimum of 95% identity and coverage. those conserved proteins were then concatenated and aligned by probcons with default options [31]. phyml 3.0 [32] was used to construct the phylogenetic tree using the maximum-likelihood method. the tree was bootstrapped 1000 times to estimate the confidence […]

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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