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# AnnoConvert #
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This command generate LiftOver Annotation based on annotation of species 1.
For help, type AnnoConvert and enter.

usage:
AnnoConvert <perl directory> <reference bed> <Sp1ToSp2_chain> <Sp2ToSp1_chain> <liftOver_minMatch> <output directory> <sp1> <sp2> <delete temp>

where:
<perl directory>: the directory where perl_lib locate (/path_to_XSAnno/bin/perl_lib)
<reference bed>: reference bed file. The annotation field of each line should include at least geneID|transcriptID|geneName|transcriptName, separated by "|"
<Sp1ToSp2_chain>: chain file convert coordinate from species 1 to species 2
<Sp2ToSp1_chain>: chain file convert coordinate from species 2 to species 1
<liftOver_minMatch>: -minMatch parameter pass to liftOver
<output directory>: output directory
<delete temp>: whether temporary directory should be deleted (Y/N)


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# BlatFilter #
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This command performs local alignment to filter orthologs.
For help, type BlatFilter and enter.

usage:
BlatFilter <Sp1.2bit> <Sp2.2bit> <Sp1Anno.bed> <Sp2Anno.bed> <inter-species ID> <inter-species PL> <paralog ID> <paralog PL> <perl directory> <output directory> <Species 1> <Species 2> <Sp1.11ooc (optional)> <Sp2.11ooc(optional)>


<Sp1.2bit>: the 2bit genome files of Species 1
<Sp2.2bit>: the 2bit genome files of Species 2
<Sp1Anno.bed>: Species 1 annotation in bed format (LiftOver Annotation)
<Sp2Anno.bed>: Species 2 annotation in bed format (LiftOver Annotation)
<inter-species PID>: BLAT Percent Identity Score between two species, value from 0 to 1. 1 mean exact match.
<inter-species PL>: Percentage of length aligned between species, value from 0 to 1
<paralog PID>: BLAT Percent Identity Score between paralogs, value from 0 to 1. 1 mean exact match.
<paralog PL>: Percentage of length aligned between paralogs, value from 0 to 1
<perl directory>: the directory where perl scripts locate
<output directory>: the directory where the output files should be write to
<Species 1>: output name of Species 1
<Species 2>: output name of Species 2
<Sp1.11ooc>: (optional) the 11ooc file of Species 1 provided for BLAT to speed up alignment
<Sp2.11ooc>: (optional) the 11ooc file of Species 2 provided for BLAT to speed up alignment

NOTE: choose loose PID and PL in this step. Further filtering will be performed using R functions.


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# liftOverBlockSim.pl #
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This perl script generates a matrix of percent of identity (PID) calculated from random sampling of short sequences in whole-genome pairwise alignment.

Usage:
perl liftOverBlockSim.pl <options>

Options:
 -i for input axt files, seperated by ","
 -o for output file
 -b for segment size
 -n for number of iterations

Output:
A matrix of percent of identity (PID). Each row represents PIDs from one iteration. Each column represents each genomic block from where the short sequences are sampled.