Description Usage Arguments Details Value Author(s) References
Identify and align core genes, concatenate the alignments in a single file, and use it to compute a phylogeny.
1 2 3 4 |
gffs |
A |
hmmFile |
The path to the |
isCompressed |
|
eval |
Consider hits with an evalue less than |
level |
|
phyloMode |
One of "nj" (Neighbour-joining) of "ml" (Maximum likelihood). |
nbs |
Number of bootstrap. If |
outDir |
Where to put the output files. If |
aliPfx |
A |
treePfx |
A |
mafftMode |
Alignment accuracy. One of "mafft", "ginsi", "linsi" or "einsi". The first one is the default MAFFT mode, very fast. The second uses mafft options "–maxiterate 1000 –globalpair". The third uses "–maxiterate 1000 –localpair" (phylen DEFAULT). The fourth uses "–ep 0 –maxiterate 1000 –genafpair". See MAFFT manual for more details. |
keepOgs |
|
n_threads |
|
... |
Further arguments to pass to optim.pml. |
This function takes gff files as returned by prokka (Seemann T, 2014) and a set of hmm models, search the models in the genomes, identifies the "core" set of genes, align and concatenates them into a "super gene" alignemnt. Once this alignment is built, a phylogeny is inferred.
HMMER 3.1b2 is used as search engine, and MAFFT aligner is used to align the orthologous groups. Both software must be installed before running this pipeline.
Note: mafft
aliases ginsi
, linsi
, and
einsi
(see above) must be also installed. This shortcuts are by
default installed together with mafft if you download and install the
software from the MAFFT webpage,
but probably not if use a package manager as apt
or brew
.
phangorn package is used to perform the phylogenetic inference.
A core genome alignment file, a phylogenetic tree in newick format
(or two, see nbs
parameter), and an object of class "phylo" on
console. Optionally, a directory with the orthologous groups used for the
alignment (see keepOgs
parameter).
Ignacio Ferres
Paradis E., Claude J. & Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.
Schliep K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics, 27(4) 592-593.
Katoh K, Standley DM. 2013. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution 30(4):772-780.
Jensen LJ, Julien P, Kuhn M, et al. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Research 36(Database issue):D250-D254.
S. R. Eddy. 2011. Accelerated profile HMM searches. PLoS Comp. Biol. 7:e1002195.
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