rmontagn / project_clustalw-based_alignment Goto Github PK

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THE CONTEXT

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Sequence alignement is an important part of Bioinformatics. It is a necessary tool for fields like phylogeny and for the "omics" methods.

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THE PROJECT

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This project aims to write a clustalW-based alignement program in Java.

The proximity between sequences and the order of alignment is assessed by UPGMA method (Unweighted Pair Group Method with Arithmetic Mean). UPGMA allows to build a dendrogram which is then used to guide sequence aligment.

Be aware that once sequences are in the same cluster, they will not be re-aligned against each other.

Input : several sequences to align in FASTA format.

Output : a graphical representation of the alignment.

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USAGE

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1. Download all the java files. The main() is in the Sequences class (with an "s")

2. In bash type : javac Sequences.java

3. Then type : java Sequences <your.fasta.file>