megaptera-package: MEGA-Phylogeny TEchniques in R
In heibl/megaptera: MEGAPhylogeny Techniques in R
Description
Details
Author(s)
References
Description
This package automates the sequence retrieval and procession from internet databases (currently Nucleotide at GenBank) to produce (possibly large) aligned nucleotide sequence datasets.
Details
Package: megaptera
Type: Package
Version: 1.1.6
Date: 2019-02-13
License: GPL (>= 2)
Welcome to megaptera!
To work with megaptera you need a functional installation of postgreSQL on your computer. Please see http://www.postgresql.org for details on installation and working with postgreSQL. Although not necessary to build datasets with megaptera, you might benefit from a basic knowledge of standard query language (SQL).
You also will need a program for multiple sequence alignment (MSA). Currently, the only option here is MAFFT and I recommend you take a look at https://mafft.cbrc.jp/alignment/software/.
In addition, poorly aligned parts of the dataset may be masked. Although optional, this step is highly recommended. Again, there is currently one single program used by megaptera: Gblocks (http://molevol.cmima.csic.es/castresana/Gblocks.html).
If you are new to megaptera, I'd suggest to take a look the package vignette.
Author(s)
Christoph Heibl
Maintainer: Christoph Heibl <christoph.heibl@gmx.net>
References
Nucleotide at NCBI: http://www.ncbi.nlm.nih.gov/nuccore
heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.
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Description Details Author(s) References
Description
This package automates the sequence retrieval and procession from internet databases (currently Nucleotide at GenBank) to produce (possibly large) aligned nucleotide sequence datasets.
Details
| Package: | megaptera |
| Type: | Package |
| Version: | 1.1.6 |
| Date: | 2019-02-13 |
| License: | GPL (>= 2) |
Welcome to megaptera!
To work with megaptera you need a functional installation of postgreSQL on your computer. Please see http://www.postgresql.org for details on installation and working with postgreSQL. Although not necessary to build datasets with megaptera, you might benefit from a basic knowledge of standard query language (SQL).
You also will need a program for multiple sequence alignment (MSA). Currently, the only option here is MAFFT and I recommend you take a look at https://mafft.cbrc.jp/alignment/software/.
In addition, poorly aligned parts of the dataset may be masked. Although optional, this step is highly recommended. Again, there is currently one single program used by megaptera: Gblocks (http://molevol.cmima.csic.es/castresana/Gblocks.html).
If you are new to megaptera, I'd suggest to take a look the package vignette.
Author(s)
Christoph Heibl Maintainer: Christoph Heibl <christoph.heibl@gmx.net>
References
Nucleotide at NCBI: http://www.ncbi.nlm.nih.gov/nuccore
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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