Archive for October, 2011

Creating Super Family Trees

This tutorial will explain how to make Super Trees using the SFT1 approach

The SFT1 approach builds a tree at the level of each TCDB sequence. To build a SFT2, instead of using getNcbiSeq.pl, you should build fasta files containing homologs for all the members of a subfamily or group, fasta files like those representing an entire TC family. After obtaining fasta files for each group that will be included in your SFT2, you would run supertree.pl.

The programs used here have recently been updated to run faster than before, to take care of some labeling problems (due to phylip‘s limitation to 10 character labels), and to run fitch and consense. These instructions reflect the new usage protocols.

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Using Ancient-Rep to find internal TMS repeat units

Ancient-Rep will find internal TMS repeats using a list of homologs.

Enter ‘ancient’ in the Terminal app to begin.

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