HaMStR: profile hidden markov model based search for orthologs in ESTs (Q33479760)

27 July 2017

title

HaMStR: profile hidden markov model based search for orthologs in ESTs (English)

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27 July 2017

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3

Arndt von Haeseler

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27 July 2017

1

Ingo Ebersberger

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27 July 2017

Sascha Strauss

2

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27 July 2017

publication date

8 July 2009

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27 July 2017

published in

BMC Evolutionary Biology

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27 July 2017

volume

9

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27 July 2017

page(s)

157

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Algorithm of OMA for large-scale orthology inference

27 July 2017

cites work

1 reference

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Broad phylogenomic sampling improves resolution of the animal tree of life

21 June 2018

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21 June 2018

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EST sequencing of Onychophora and phylogenomic analysis of Metazoa

21 June 2018

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Assessing performance of orthology detection strategies applied to eukaryotic genomes

21 June 2018

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Orthology prediction at scalable resolution by phylogenetic tree analysis

21 June 2018

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Inferring angiosperm phylogeny from EST data with widespread gene duplication

21 June 2018

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A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

21 June 2018

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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

21 June 2018

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Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

21 June 2018

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Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles).

21 June 2018

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Phylogenomics and the reconstruction of the tree of life

21 June 2018

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Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia

21 June 2018

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MAFFT version 5: improvement in accuracy of multiple sequence alignment

21 June 2018

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21 June 2018

GeneWise and Genomewise

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OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

21 June 2018

1 reference

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TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets

21 June 2018

1 reference

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RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs

21 June 2018

1 reference

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TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2723089

BLAT—The BLAST-Like Alignment Tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2723089

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2723089

The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species

21 June 2018

1 reference

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The COG database: new developments in phylogenetic classification of proteins from complete genomes

21 June 2018

1 reference

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Base-calling of automated sequencer traces using phred. II. Error probabilities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2723089

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2723089

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2723089

Distinguishing Homologous from Analogous Proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2723089

Assessment of phylogenomic and orthology approaches for phylogenetic inference.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2723089

Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2723089

Automatic clustering of orthologs and inparalogs shared by multiple proteomes.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2723089

LUCY2: an interactive DNA sequence quality trimming and vector removal tool.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2723089

PartiGene--constructing partial genomes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2723089

31 October 2018

Identifiers

DOI

10.1186/1471-2148-9-157

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Dimensions Publication ID

27 July 2017

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https://scigraph.springernature.com/pub.10.1186/1471-2148-9-157

9 September 2019

1 reference

27 July 2017

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