Web Service Phylogenetics_AT_JST REST It

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Annotations: 22 Total number of annotations from the provider's definition / description document. 0 Total number of annotations submitted by members of BiodiversityCatalogue. 22 Total number of annotations sourced from other registries. 0

REST Endpoints (17)

Quick Browse | Alignment: GET /InsertJobs?NAME=HMMSearchAlign_Pmerge | GET /InsertJobs?NAME=MadTranslator45 | MsaPAD | Bayesian Phylogenetic inference: Consensus Tree | MCMCMC_Convergence | Posterior Predicitve Test for MrBayes | MrBayes Phylogenetic inference on 16CPUs | PartitionFinder | Resubmission MrBayes | General purpose Phylogenetic inference: TreeVisualization@ITOL | JobRetrival: GET /SelectJob | GET /SelectJobs | Maximum Likelihood Phylogenetic inference: RAXML_boot | RAXML_boot_Mapping | Raxml_partition | Phylogenetic Diversity: phylocom | PhyloH |

Alignment

GET /InsertJobs?NAME=HMMSearchAlign_Pmerge

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Alignment

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=HMMSearchAlign_Pmerge&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Bachir (almost 3 years ago)

It searches, using hmmsearch (HMMer3.0 package), translated amino acid sequences against a mirror of PFAM-A conserved domains database. It performs a MSA of either single or multiple protein domains coding sequences. Sequences not coding for the same domain/s of the majority of sequences and those not following domains succession (just in case of multiple domains coding sequences) are discarded. A custom Python2.7 script retrieves then the relevant information regarding domain position falling within or on a complete sequence to align each sequence or fragment of it against its corresponding PFAM domain profile. Furthermore, all fragments are assembled to produce a multiple domain DNA alignment, by back translating protein alignments. The back-translated DNA alignments are merged together to construct the whole multiple domains alignment. During merging, aligned DNA blocks are added from 5‘ to 3’, and if sites do overlap across domain, the 3‘ overlapping domain section is discarded and registered in a separate file as well as sites that do not match any domain.

Tags on this endpoint:

GET /InsertJobs?NAME=MadTranslator45

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Alignment

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=MadTranslator45&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Bachir (almost 3 years ago)

It translates DNA sequences following a user defined genetic code and reading frame(s). It devides the translated sequence at each stop codon into separate sequences. The genetic code and the frame are tracked by adding their information to the sequence ID for easier parsing procedure.

Tags on this endpoint:

MsaPAD | GET /InsertJobs?NAME=MsaPAD

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Alignment

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=MsaPAD&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Bachir (almost 3 years ago)

It translates DNA sequences following a user defined genetic code and reading frame(s). It devides the translated sequence at each stop codon into separate sequences. It searches, using hmmsearch (HMMer3.0 package), translated amino acid sequences against a mirror of PFAM-A conserved domains database. It performs a MSA of either single or multiple protein domains coding sequences. Sequences not coding for the same domain/s of the majority of sequences and those not following domains succession (just in case of multiple domains coding sequences) are discarded. A custom Python2.7 script retrieves then the relevant information regarding domain position falling within or on a complete sequence to align each sequence or fragment of it against its corresponding PFAM domain profile. Furthermore, all fragments are assembled to produce a multiple domain DNA alignment, by back translating protein alignments. The back-translated DNA alignments are merged together to construct the whole multiple domains alignment. During merging, aligned DNA blocks are added from 5‘ to 3’, and if sites do overlap across domain, the 3‘ overlapping domain section is discarded and registered in a separate file as well as sites that do not match any domain.

Tags on this endpoint:

Bayesian Phylogenetic inference

Consensus Tree | GET /InsertJobs?NAME=consensus_xml

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Bayesian Phylogenetic inference

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=consensus_xml&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Saverio Vicario (about 3 years ago)

Technical service description: python script taken from http://testjst.ba.infn.it/software/consensus2.1XML.py that compute consensus tree over the posterior distribution tree and compute branch length average only among bipartition present in the consensus topology.

Tags on this endpoint:

MCMCMC_Convergence | GET /InsertJobs?NAME=geoks_xml

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Bayesian Phylogenetic inference

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=geoks_xml&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Saverio Vicario (over 3 years ago)

Estimate the probability of convergence for a phylogenetic inference performed with MrBayes by comparing the degree of overlap among different indipendent run of MrBayes on the same data and model. is based on GeoKS software.

Tags on this endpoint:

Posterior Predicitve Test for MrBayes | GET /InsertJobs?NAME=MrBayesPPtest

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Bayesian Phylogenetic inference

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=MrBayesPPtest&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Saverio Vicario (almost 3 years ago)

Main title

Perform a posterior predictive test sensu Bollback, 2002;http://mbe.oxfordjournals.org/content/19/7/1162.full) on the partitioned model.

Tags on this endpoint:

MrBayes Phylogenetic inference on 16CPUs | GET /InsertJobs?NAME=MrBayes_16CPUs

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Bayesian Phylogenetic inference

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=MrBayes_16CPUs&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Saverio Vicario (about 3 years ago)

Perfrom a phylogenetic inference with mrbayes 3.2.1.

Tags on this endpoint:

PartitionFinder | GET /InsertJobs?NAME=PartitionFinder

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Bayesian Phylogenetic inference

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=PartitionFinder&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Saverio Vicario (over 3 years ago)

Using PartitionFinder and uploading annotation of partitions and mutlifasta MSA’s the service indicates best partitioned models for the data assuming a given range of possible partition models selected using AIC/AICc/BIC approach. Technical service description: PartitionFinder 1.0.1 python code was taken from the web site http://www.robertlanfear.com/partitionfinder/, while the phyml version used in the service was directly given by Stephane Guidon (developer of phyloml) given that no linux binary of the software was otherwise available. The python interpreter used is a python2.7. All Partitionfinder option are accessible. Note that Partitionfinder aminoacid was not installed.

Tags on this endpoint:

Resubmission MrBayes | GET /InsertJobs?NAME=Re_MrBayes_16CPUs

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Bayesian Phylogenetic inference

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=Re_MrBayes_16CPUs&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Saverio Vicario (almost 3 years ago)

Perfrom a phylogenetic inference with mrbayes 3.2.1 using as input a previous run of mrbayes

Tags on this endpoint:

General purpose Phylogenetic inference

TreeVisualization@ITOL | GET /InsertJobs?NAME=itol

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: General purpose Phylogenetic inference

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=itol&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Saverio Vicario (about 3 years ago)

Takes a tree in newick format and visualize the content, including branch support on http://itol.embl.de/

Tags on this endpoint:

JobRetrival

GET /SelectJob

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: JobRetrival

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/SelectJob?IdJob={IdJob}

by Saverio Vicario (over 3 years ago)

All endpoints of this service that have tag method, submit a job to JST webservice. This endpoint is the unique place where results could be retrieved using the number taken from the body of the tag “jobID” in the response for a job submission.

Tags on this endpoint:
none

GET /SelectJobs

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: JobRetrival

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/SelectJobs?FLAG={FLAG}

by Saverio Vicario (over 3 years ago)

All endpoints of this service that have tag method, submit a job to JST webservice. This endpoint is the unique place where results could be retrieved using the number taken from the body of the tag “flag” in the response for a job submission. Flag number group several jobid, incase that a job submission sponded several subtasks

Tags on this endpoint:
none

Maximum Likelihood Phylogenetic inference

RAXML_boot | GET /InsertJobs?NAME=RAXML_boot_An

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Maximum Likelihood Phylogenetic inference

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=RAXML_boot_An&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Saverio Vicario (almost 3 years ago)

perform a bootstrap analysis

Tags on this endpoint:

RAXML_boot_Mapping | GET /InsertJobs?NAME=RAXML_boot_Ma

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Maximum Likelihood Phylogenetic inference

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=RAXML_boot_Ma&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Saverio Vicario (almost 3 years ago)

add bootstrap value to a previous phylogenetic inference

Tags on this endpoint:

Raxml_partition | GET /InsertJobs?NAME=Raxml_partition

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Maximum Likelihood Phylogenetic inference

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=Raxml_partition&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Saverio Vicario (almost 3 years ago)

perform a search of best maximum likelihood tree with raxml using a partitioned model

Tags on this endpoint:

Phylogenetic Diversity

phylocom | GET /InsertJobs?NAME=phylocom

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Phylogenetic Diversity

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=phylocom&arguments={arguments}&mail={mail}&sessionId={sessionId}

Tags on this endpoint:

PhyloH | GET /InsertJobs?NAME=PhyloH

Part of Service: Phylogenetics_AT_JST

Part of Endpoint Group: Phylogenetic Diversity

Template: Help_icon http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob/InsertJobs?NAME=PhyloH&arguments={arguments}&mail={mail}&sessionId={sessionId}

by Saverio Vicario (almost 3 years ago)

Partitioning the total entropy of a data set, named γ, in intra-groups, called α, and inter-groups, called β components. The entropy use is the phylogenetic entropy sensu Chao et al.(2010) that take in account how the object observed are not all equally different from each other but they have a dissimilarity structure described the user supplied phylogeny.

by Saverio Vicario (over 2 years ago)

If you want to try the service you could use the istance loaded on the portal

Tags on this endpoint:

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