MultiPhyl protocols

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MultiPhyl specifications

Information


Unique identifier OMICS_15839
Name MultiPhyl
Interface Web user interface
Restrictions to use None
Input format FASTA, PHYLIP
Computer skills Basic
Stability No
Maintained No

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This tool is not available anymore.

Publication for MultiPhyl

MultiPhyl in pipelines

 (2)
2010
PMCID: 2997564
PMID: 20889655
DOI: 10.1093/gbe/evq062

[…] with the gblocks program () with the minimal length of a block set at six amino acid positions, and the maximum number of allowed contiguous nonconserved amino acid positions set at 20. the program multiphyl (), which selects the best of 88 amino acid substitution models, was used to reconstruct the maximum likelihood (ml) tree of each cluster. the nuts are defined as trees from cogs […]

2006
PMCID: 1679813
PMID: 17121679
DOI: 10.1186/1471-2148-6-99

[…] for the presence of evolutionary signal better than random (p < 0.01). we found that 511 alignments failed the ptp test; therefore 4,805 were used for phylogenetic reconstruction analysis. using multiphyl [] appropriate protein substitution models were selected and used to reconstruct ml phylogenies for each individual gene family. bootstrap resampling was carried out 100 times […]


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MultiPhyl in publications

 (10)
PMCID: 3630104
PMID: 23637636
DOI: 10.1371/journal.pgen.1003471

[…] snps, a maximum likelihood tree was inferred using phyml applying the tvm+g model, which had the best-fit of sequence evolution according to the akaike information criterion (aic) using multiphyl . linear regression of root-to-tip distances against date of isolation was performed using path-o-gen (http://tree.bio.ed.ac.uk/software/pathogen/)., the population history of the agona […]

PMCID: 3402446
PMID: 22911845
DOI: 10.1371/journal.pone.0041697

[…] proportion of invariable sites (0.40), and alpha parameter of gamma distribution (0.55). maximum likelihood trees (ml) were constructed by using the nearest neighbor interchange tree search with multiphyl software . neighbor-joining (nj) trees were constructed with paup* version 4.0b10 . sequence variation and substitution pattern of the 1.5 kb mtdna fragment were analyzed using the program […]

PMCID: 3197165
PMID: 21562596
DOI: 10.1038/ismej.2011.53

[…] of constrained and unconstrained trees were calculated with raxml 7.0.3 () using the protmixwagf setting, an implementation of the wag+g model of amino-acid sequence evolution (), as selected with multiphyl v1.0.6 (). single-site likelihoods were calculated in raxml using the protgammawagf setting and imported into consel 0.1i () to compare the tree topologies by a series of statistical tests, […]

PMCID: 3068965
PMID: 21406099
DOI: 10.1186/1471-2148-11-71

[…] with opal[] and the results were manually inspected. the best-fitting substitution model was selected using modelgenerator [], under the akaike information criterion (aic1), as implemented in multiphyl online[]. the following models were integrated in the phylogenetic analysis: gtr + i + g for c-alpha; hky + i for hs3 and hs4; hky + g for hs1.2., an unrooted tree was constructed using […]

PMCID: 3268564
PMID: 22303303
DOI: 10.3389/fgene.2011.00004

[…] billion and is steadily increasing (eadline, ). in bioinformatics, many interesting applications have emerged. the following are a few examples. a high-throughput distributed phylogenetics platform, multiphyl, has been developed, which is capable of using the idle computational resources of many heterogeneous non-dedicated machines to form a phylogenetics supercomputer (keane et al., ). […]


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MultiPhyl funding source(s)
Supported by the Irish research council for Science, Engineering and Technology.

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