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PhyloGena specifications

Information


Unique identifier OMICS_08884
Name PhyloGena
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages Java
Computer skills Medium
Version 1.04
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Klaus Valentin

Publication for PhyloGena

PhyloGena citations

 (6)
library_books

BIR Pipeline for Preparation of Phylogenomic Data

2015
Evol Bioinform Online
PMCID: 4412416
PMID: 25987827
DOI: 10.4137/EBO.S10189

[…] Some of the steps in the BIR pipeline are similar to those of the other bioinformatics applications such as PyPhy, PhyloGena, Hal, and bioinformatics services such as phylogeny.fr and PALM. However, BIR is unique in providing a sequence screening using seed alignments to generate gene alignments. Also, it is the o […]

library_books

Workflow management systems for gene sequence analysis and evolutionary studies – A Review

2013
Bioinformation
PMCID: 3732438
PMID: 23930017
DOI: 10.6026/97320630009663

[…] onal tools used for performing different tasks in this process. Major workflows for phylogenetic analysis along with important tools which are integrated are compared in (see supplementary material).Phylogena [] is a user-friendly, interactive graphical user interface running on desktop computers that automatically performs a Basic Local Alignment Search Tool (BLAST) with respect toquery sequence […]

library_books

Current opportunities and challenges in microbial metagenome analysis—a bioinformatic perspective

2012
Brief Bioinform
PMCID: 3504927
PMID: 22966151
DOI: 10.1093/bib/bbs039

[…] c information from the resulting hits. This can be done either by constructing a multiple sequence alignment from the best matching hits with subsequent phylogenetic reconstruction, as implemented in Phylogena [], or it can be done directly based on the BLAST results. Of course, as BLAST is a heuristic for fast sequence database searches and not a phylogenetic algorithm per se, the top BLAST hit d […]

library_books

Comparative gene expression in toxic versus non toxic strains of the marine dinoflagellate Alexandrium minutum

2010
BMC Genomics
PMCID: 2874808
PMID: 20403159
DOI: 10.1186/1471-2164-11-248

[…] her expressed in the toxic strains at both time points, 49 could be manually annotated based on BLAST-based automated annotation, domain comparison using Pfam and phylogenetic reconstruction with the PhyloGena program []. Putative functions could be assigned to 31 of these genes (Table ).The group of 47 genes higher expressed in the non-toxic strain AL1T contained 8 genes for which a putative func […]

library_books

TARGeT: a web based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences

2009
Nucleic Acids Res
PMCID: 2699529
PMID: 19429695
DOI: 10.1093/nar/gkp295

[…] eral automated pipelines have been developed to ease homolog identification and most are limited to protein or expressed sequence tag (EST) databases. For example, PhyloBLAST (), Pyphy (), HoSeql (), PhyloGena () and TRIBE-MCL () perform BLASTP searches and retrieve data from protein databases. SimESTs uses TBLASTN to search EST databases (). Because these programs only compare protein-coding sequ […]

library_books

Identification of proteins involved in the functioning of Riftia pachyptila symbiosis by Subtractive Suppression Hybridization

2007
BMC Genomics
PMCID: 2175520
PMID: 17892591
DOI: 10.1186/1471-2164-8-337

[…] s sequences were performed on the NCBI server. The assembled sequences were analyzed for homology with known sequences in databases using the BlastX and BlastN programs [[]] and also treated with the PhyloGena software [[]] which combines both homology searching and phylogenetic reconstruction to verify the homology attributions.The redundancy corresponds to the probability that a newly sequenced […]

Citations

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PhyloGena institution(s)
Center for Computing Technologies (TZI), Bremen, Germany; Urbanstr., Berlin; Technology Transfer Centre (TTZ/BIBIS), An der Karlstadt, Bremerhaven, Germany; Alfred Wegener Institute, Am Handelshafen, Bremerhaven, Germany

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