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genoplotr_wrapper's Introduction

genoPlotR_wrapper

Wrapper for the genoPlotR R package. This is a wrapper that makes the use of genoPlotR easier, I have not created genoPlotR!

GenoPlotR makes a gene synteny plot, but pre-processing of data is necessary. This wrapper makes phylogeny, genbank files and blast comparisons that is needed for the genoPLotR package.

Dependencies are mafft, raxmlHPC, python, biopython, prokka, blastn and the R pacakges genoPlotR, ape and ade4.

The input is a multifasta file.

sh recomb_genoplotR_wrapper.sh multifasta

The output is a pdf file with the gene synteny plot

output example:

alt tag

genoplotr_wrapper's People

Contributors

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Forkers

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genoplotr_wrapper's Issues

error convert_fasta2phylip.pl

Hi, I got this error

Can't open perl script "/data/data5/Projects/thomas/scripts/convert_fasta2phylip.pl": No such file or directory

Can't find this script at your release.

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