BranchClust: a phylogenetic algorithm for selecting gene families

doi:10.1186/1471-2105-8-120

BMC Bioinformatics

Volume 8

Viewing options:

Abstract
Full text
PDF (1.1MB)
Additional files

Associated material:

Related literature:

Articles citing this article
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

Poptsova MS
Gogarten JP

on PubMed

Poptsova MS
Gogarten JP
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Methodology article

BranchClust: a phylogenetic algorithm for selecting gene families

Maria S Poptsova and J Peter Gogarten

Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA

author email corresponding author email

BMC Bioinformatics 2007, 8:120doi:10.1186/1471-2105-8-120


Published:	10 April 2007

Additional files

Additional file 1:

ATP synthase superfamily for 13 gamma proteobacteria. Superfamily of ATP synthases alpha and beta subunits, flagella and type III secretion system ATPases, and Rho-termination factors. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: JPEG Size: 27KB Download file

Additional file 2:

ATP synthase superfamily for 30 bacteria and archaea. Superfamily of ATP synthases alpha and beta subunits, flagella and type III secretion system ATPases, and Rho-termination factors. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 10.

Format: JPEG Size: 61KB Download file

Additional file 3:

ATP synthase superfamily for 317 bacteria and archaea. Superfamily of ATP synthases alpha and beta subunits, flagella and type III secretion system ATPases, and Rho-termination factors. The superfamily was assembled by on-to-all BLAST searches using genome of Escherichia coli K12 as a starting genome; BranchClust was applied with MANY/FEW = 150.

Format: JPEG Size: 52KB Download file

Additional file 4:

Superfamily of cell division proteins, ribonucleases E, ATP synthase chain B and hypothetical proteins for 13 gamma proteobacteria. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 180KB Download file

Additional file 5:

Superfamily DNA topoisomerase IV subunit B and DNA gyrase subunit IV for 13 gamma proteobacteria. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 37KB Download file

Additional file 6:

Superfamily of signal recognition particle proteins, chromosomal replication initiators, insertion sequence protein for 13 gamma proteobacteria. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 190KB Download file

Additional file 7:

Superfamily of elongation factors, peptide chain release factors and GTP-binding proteins for 13 gamma proteobacteria. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 323KB Download file

Additional file 8:

Superfamily of methyltransferases for 13 gamma proteobacteria. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 131KB Download file

Additional file 9:

Superfamily of universal stress protein and amino-acid transporters for 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 243KB Download file

Additional file 10:

Superfamily of kinases for 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 52KB Download file

Additional file 11:

Superfamily of aminotransferases for 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 227KB Download file

Additional file 12:

Superfamily of potential transcriptional regulators for 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 80KB Download file

Additional file 13:

Superfamily of potential transcriptional regulators for 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 287KB Download file

Additional file 14:

Superfamily of reductases, dehydrogenases, NADH oxidases for 16 bacteria and 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 24.

Format: PNG Size: 341KB Download file

Additional file 15:

Superfamily of translation elongation factors, peptide chain release factors and GTP-binding proteins for 16 bacteria and 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 24.

Format: PNG Size: 255KB Download file

Additional file 16:

Superfamily of replication factors C and DNA polymerases III for 16 bacteria and 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 24.

Format: PNG Size: 52KB Download file

Additional file 17:

Superfamily of ATP dependent RNA and DNA helicases for 16 bacteria and 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 24.

Format: PNG Size: 187KB Download file

Additional file 18:

Superfamily of ABC transporters for 16 bacteria and 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 24.

Format: PNG Size: 1.4MB Download file