MiREvo: A platform for miRNA evolution analysis


Overview:
miREvo: is an integrated platform for miRNA expression evaluation, novel miRNA predtion both for plants and animals and homology sequence gene search platform.

To support homology identification in plant kingdom, we also provide whole genome alignment for 11 plants species including Arabidopsis, Oryza sativa, etc.

To take a look at the command line parameters and available tools using:
miREvo or miREvo_tk
Further information on each of the tools can be retrieved by the command pattern:
miREvo "toolname"
for instance, in the step of the filter sequencing reads:
miREvo filter

miREvo can either operates via a Graphical User Interface (GUI) or from the command-line interface (CLI). The options and parameters in the GUI are almost the samve as the (CLI). The GUI also provides as a graphical interface to view many of the results and results can be more lively presented in GUI. You can also use the GUI to view your the result run from command-line interface.
whether the project was assembled using the GUI or the CLI. Results appear as output files using either the GUI or the CLI.



Download:
miREvo v1.1 readme
For Linux, extract: tar zxvf miREvo_v1.1.tar.gz
utilities readme
Some utilities, such as mafsInRegion, fastq2fasta.pl, etc.
dme demo
Demo for Drosophila melanogaster, extract: tar zxvf dme_demo.tar.gz
dsi demo
Demo for Drosophila simulans, extract: tar zxvf dsi_demo.tar.gz
ath demo
Demo for Arabidopsis thaliana, extract: tar zxvf ath_demo.tar.gz
Comparing orthologs expression readme
Demo for compare the expression of othologous miRNA acorss 3 Drosophila speices, extract: tar zxvf dro_orth_exp.tar.gz
dm3 maf readme
Multiple alignments of 14 insects genomes with D. melanogaster
ce10 maf readme
Multiple alignments of 6 worms with C. elegans
hg19 maf readme
Multiple alignments of 45 vertebrate genomes with Human
tair8-11species maf readme
Multiple alignments of 11 green plant genomes with A. thaliana
osaInd1-osaJap1 maf readme
Pairwise alignments between two rice subspece: Indica (9311) and Japonica(tigr6.0)
plant parameters
parameters for new plant miRNA prediction