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Protocols

SCaFoS specifications

Information


Unique identifier OMICS_25680
Name SCaFoS
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Medium
Version 1.2.5
Stability Stable
Source code URL http://megasun.bch.umontreal.ca/Software/scafos/version/scafos_src_linux.125.tgz
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Béatrice Roure
  • person_outline [email protected]
  • person_outline Hervé Philippe

Publication for SCaFoS

SCaFoS citations

 (29)
library_books

A phylogenomic framework and timescale for comparative studies of tunicates

2018
BMC Biol
PMCID: 5899321
PMID: 29653534
DOI: 10.1186/s12915-018-0499-2

[…] ned for each curated gene alignment and were further sought by a visual examination of each individual gene phylogeny.The concatenation of the resulting 258 amino acid alignments was constructed with SCaFoS [] by defining 63 deuterostomian operational taxonomic units (OTUs) representing all major lineages. The taxon sampling included 18 tunicates, 34 vertebrates, and one cephalochordate, with seve […]

library_books

A software tool ‘CroCo’ detects pervasive cross species contamination in next generation sequencing data

2018
BMC Biol
PMCID: 5838952
PMID: 29506533
DOI: 10.1186/s12915-018-0486-7

[…] phore transcriptomic data from that study (i.e. dataset A, for which the cross contamination network is shown in Fig. ) using Forty-Two (available at https://bitbucket.org/dbaurain/42/). We then used SCaFoS [] to concatenate the 114 completed alignments into a supermatrix, selecting the longest sequence if several sequences were present for a given species. We used RAxML [] with the LG + Γ4 + F mo […]

library_books

Phylotranscriptomic consolidation of the jawed vertebrate timetree

2017
PMCID: 5584656
PMID: 28890940
DOI: 10.1038/s41559-017-0240-5

[…] r more (2DP) deep paralogs. Sequence stretches with unusually low similarity (usually due to frame shifts) were masked with HMM-cleaner (R. Poujol) and alignments were trimmed. For each gene, we used SCaFoS to merge conspecific sequences and resolve putative remaining paralogy. A third decontamination step used extremely long branches estimated on a fixed reference tree as proxy for contamination. […]

library_books

Co Option and De Novo Gene Evolution Underlie Molluscan Shell Diversity

2017
Mol Biol Evol
PMCID: 5400390
PMID: 28053006
DOI: 10.1093/molbev/msw294

[…] gene families that still had taxa with multiple sequences were visually inspected and excluded if orthology was unable to be determined. Remaining alignments were concatenated into a supermatrix with ScaFoS v1.2.5 ().Phylogenomic analyses were conducted using Maximum Likelihood (ML) in RAxML v8.0.2 () and Bayesian Inference (BI) in Phylobayes MPI-version 1.5a (). Leaf stability and taxonomic insta […]

call_split

Phylogenomic analysis of Balantidium ctenopharyngodoni (Ciliophora, Litostomatea) based on single cell transcriptome sequencing

2017
PMCID: 5684829
PMID: 29134943
DOI: 10.1051/parasite/2017043
call_split See protocol

[…] lock 0.91b (−t = d, −b2 = 0.65, −b3 = 10, −b4 = 5, −b5 = a) to detect and trim the ambiguously aligned regions []. The 132 individual alignments of the 27 taxa were concatenated into a supermatrix by SCaFoS software version 4.42 using the data set assembling panel []. The maximum-likelihood (ML) analysis and Bayesian inference (BI) analysis followed Feng et al. []. For ML analysis, the concatenate […]

library_books

Comprehensive Transcriptome Analysis Provides Evidence of Local Thermal Adaptation in Three Loaches (Genus: Misgurnus)

2016
Int J Mol Sci
PMCID: 5187763
PMID: 27886141
DOI: 10.3390/ijms17121943

[…] All trimmed nucleotide sequence alignments were concatenated into superalignments for the phylogenetic analyses, with the SCaFoS program []. The phylogenetic trees were inferred from the concatenation of 1392 one-to-one orthologous genes (OGs) using the maximum likelihood (ML) and neighbor joining (NJ) methods with 1000 […]

Citations

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SCaFoS institution(s)
Canadian Institute for Advanced Research, Centre Robert Cedergren, Département de biochimie, Université de Montréal, Montréal, QC, Canada

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