README.md

In LucasBusta/phyloChemistry: Chemical and Sequence Analyses in a Phylogenetic Context

phylochemistry: integated analyses of chemical and sequence data in the context of phylogeny

phylochemistry is a set of functions for chemical and genomic/transcriptomic analysis. These tools are provided though a combination of new functions and wrapped features of previously developed packages. A number of new functions to streamline analyses in this interdisciplinary space are also provided. This repository contains the latest version of the phylochemistry R package.

INSTALL

phylochemistry is currently only available from this page. Install it using devtools:

devtools::install_github("LucasBusta/phylochemistry", quiet = FALSE, force = TRUE)
packages <- c("phylochemistry")
lapply(packages, require, character.only = TRUE)

VIGNETTE

The phylochemistry package is documented in this vignette.

NEW FEATURES

1. A Shiny app for GC-FID and GC-MS data analysis.
2. Open reading frame extraction from multiple fasta files.
3. Store BLAST results in a .csv file.
4. Minor ticks for ggplot2 axes.
5. Phylogenetic signal for discrete traits.
6. Analyze multiple sequence alignments for sites associated with user-defined function

WRAPPED FEATURES

1. BLAST transcriptomes, via NCBI BLAST+.
2. Multiple sequence alignments and codon alignments of amino acid and nucleotide sequences, via msa and orthologr.
3. Phylogenetic tree construction (including g-blocks trimming, pruning, ancestral states reconstruction), via phangorn.
4. Systematic read/write functions (csv, newick, wide tables, fasta, summary statistic tables, GFFs, chromatograms, mass spectra).
5. Phylogenetic signal for continuous traits.

LucasBusta/phyloChemistry documentation built on Sept. 6, 2020, 11:36 p.m.