Pyrotools statistics

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Pyrotools specifications


Unique identifier OMICS_19881
Name Pyrotools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++
Computer skills Advanced
Stability Stable
GCC49, Samtools, Bamtools, Seqtk, Bedtools, Vcftools, NGSUtils, SSW Library, Bowtie2
Maintained Yes


  • GraphReAlign
  • IndelCall
  • ProbAlign
  • SnpCall
  • StrainBinning
  • StrainCall



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  • person_outline Rui Jiang <>
  • person_outline Ting Chen <>
  • person_outline Feng Zeng <>

Publications for Pyrotools

Pyrotools in publications

PMCID: 5873917
PMID: 29467189
DOI: 10.1534/g3.118.200040

[…] ). the sequences were used as queries to search ncbi and phytozome () databases for sofl homologs using blastp option using a < 1 x 10-2 cut-off value. the amino acid sequences were aligned using probalign v1.3 () on cipres science gateway server (). bayesian inference analysis was performed with the mr. bayes 3.2.1 on xsede tool on cipres science gateway for 30 million generations with 8 […]

PMCID: 5278576
PMID: 28132643
DOI: 10.1186/s12864-016-3411-x

[…] for testing positive selection. a further 400 mcl clusters were unable to produce alignments that contained continuous sequence for all eight species, leaving 932 genes that were used as input for probalign to build consensus quality alignments. probalign does an additional filtering by removing poor quality alignments, and we further required all alignments to cover > 50% of the sites […]

PMCID: 4852290
PMID: 27200066
DOI: 10.3389/fpls.2016.00598

[…] nonetheless, the resolution was slightly improved and the positions of most genes were better congruent with angiosperm phylogeny. in contrast, the dataset created based on an alignment produced by probalign only included 696 sites, among which 591 were informative (dataset ). moreover, in the resulting phylogenetic tree, the positions of some major plant groups were discordant with angiosperm […]

PMCID: 4007547
PMID: 24625962
DOI: 10.1093/gbe/evu048

[…] parameter of 1.8. simulations have shown this value to be generally robust to false positives and negatives (). nucleotide sequences corresponding to each mcl gene cluster were aligned using probalign v1.1 ()., for the phylogenetic analysis, we selected those mcl gene clusters that were shared among all taxa and contained only single gene copies for each taxon (the core set) (n = 159) […]

PMCID: 3546061
PMID: 23151128
DOI: 10.1186/1471-2164-13-622

[…] rrna gene fragments from b. bovis (eu075182) and t. parva (z23263) were used as a query under suggested algorithm parameters [] in ncbi blast 2.2 []. in silico analysis was also performed with probalign beta version 1.2 [] and ssearch 3.5 [] using known rrna gene fragments and suggested advanced search options [,]. newly identified candidate rrna genes were, likewise, used as input […]

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Pyrotools institution(s)
Xiamen University, Siming Qu, Xiamen Shi, China; Tsinghua University, Haidian Qu, Chine; University of Southern California, Los Angeles, CA, USA

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