megaptera (version 1.0-0)

MEGAPhylogeny Techniques in R

Description

Given a set of taxa and marker, the goal is build a complete and correct sequence alignment for phylogenetic analysis.

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Version

Install

install.packages('megaptera')

Monthly Downloads

Version

1.0-0

License

GPL (>= 2)

Maintainer

Christoph Heibl

Last Published

November 13th, 2014

Functions in megaptera (1.0-0)

cetacea

Cetacea Phylogeny

stepB

Step B: Search and Download Sequences

dbUpdateTaxonomy

Taxonomy Table

dbPars

Set Database Parameters

taxon

Definition of Species/Higher Taxa

locus

Locus/Phylogenetic Marker Definition

stepE

Step E: Calculate Each Accession's Distance from Benchmark

stepH

Step H: Detect and Separate Unalignable Blocks

dbPars-class

Class "dbPars"

io.dna.db

Read and Write DNA Sequences from/to PgSQL Database

locus-class

Class "locus"

megapteraPars-class

Class "megapteraPars"

NCBIeaa

NCBI Extended Amino Acid

stepF

Step F: Select Sequences and Assemble FASTA file

setLocus

Set locus in megapteraProj

stepC

Step C: Align Conspecific Sequences

stepD

Step D: Calculate Benchmark Sequences

stepA

Step A: Download a NCBI Taxonomy

ncbiTaxonomy

NCBI Taxonomy Database

prune.phylo.rank

Prune Phylogenies

megaptera-internal

Internal MEGAPTERA Functions

check.Functions

Check SUSILI Results

stepG

Step G: Profile Alignment

strip.infraspec

Truncation of Species Names

dbReadTaxonomy

Taxonomy of Species Contained in SQL Database

fleshoutGuidetree

Add Missing Species to a Phylogenetic Tree

megapteraProj-class

Class "megapteraProj"

taxon-class

Class "taxon"

megapteraPars

Set Pipeline Parameters

megaptera-package

MEGAPhylogenie TEchniques in R

addTip

Add Tips to a Phylogeny

megapteraProj

Bundle Input Data for the Pipeline