What is a software for phylogenetic analysis (SNPs) to use on fastq files?

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David Parra

Try with MEGA.

http://www.megasoftware.net/

Is one of the most populars and maybe, the best

Ilya Korotetskiy

There are many different software for analyse NGS data.

You can try to use SeqMan Pro or MegAlign Pro from DNAStar software package. (http://www.dnastar.com/)

Also you can try with Unipro UGENE (http://ugene.unipro.ru/)

Mauve (http://asap.ahabs.wisc.edu/software/) - is a system for efficiently constructing multiple genome alignments.

MEGA software - as mentioned above for constructing phylogenetic trees.

And many many other...

Mahadev Asaram Jadhav

you can use MrBayes for phylogenetic analysis.

http://mrbayes.sourceforge.net/