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#! /bin/sh
# This script demonstrates using LAST and maf-join to construct a
# multiple alignment of the human, mouse, chicken, and fugu
# mitochondrial genomes.
# You have to run this from inside the examples directory, else it
# won't find the files.
# Put the LAST programs and scripts into the command search path:
PATH=$PATH:../bin
# Make a LAST database of the human sequence:
lastdb -c humanMito humanMito.fa
# Align the mouse sequence to the human sequence:
lastal -pHUMSUM -j4 --split humanMito mouseMito.fa | maf-sort > hm.maf
# Align the chicken sequence to the human sequence:
lastal -pHUMSUM -j4 --split humanMito chickenMito.fa | maf-sort > hc.maf
# Align the fugu sequence to the human sequence:
lastal -pHUMSUM -j4 --split humanMito fuguMito.fa | maf-sort > hf.maf
# Join the pairwise alignments into a multiple alignment:
maf-join hm.maf hc.maf hf.maf
# Clean up the intermediate files that we made:
rm humanMito.??? h?.maf
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