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Table 1 Custom tools* currently in the main divisions of EGenBio

From: EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity

Division

Tool Name

Tool Description

Genomics

SearchSequence

Search the mtDNA genome database for DNA or protein sequences

Genomics

SearchAlignment

Search the mtDNA genome database for sequence alignments

Genomics

SearchHuSequence

Search the human mtDNA database for DNA or protein sequences

Genomics

SearchHuAlignment

Search the human mtDNA database for sequence alignments

Evolution

TranslateTree

Translate labels of a tree file

Evolution

FilterViz

Visualize filters associated with alignments

Evolution

TreeReader

Extract tree clusters along with information on branch lengths

Evolution

SaturationTool

Visualize results from saturation mutagenesis MCMC analysis

Evolution

LnLCorr

Detect coevolution among residues using LRTs and trees

Biodiversity

SpeciesList

List species currently in EGenBio

Biodiversity

SpeciesSearch

Search species by taxonomic group or NCBI genome identifier

Biodiversity

LocusOrder

Display mitochondrial gene order for specified taxa

Biodiversity

DatabaseSummary

Provide information about the EGenBio databases

Biodiversity

PrimerPermuter

Generate permutations for use in primer design

Biodiversity

PrimerAlternatives

Produce degenerate primers that reflect amino acid variation

  1. *All tools listed are original to EGenBio, except that alignments are based on ClustalW [11].