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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

9

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