G-Blocks for Trimming MSA

Question

[tony]

Hello,

I want to use G-blocks to trim a Multiple Sequence Alignment. I wanted to know what file formats are available for export after I perform the trim in G-blocks?

Also wanted to know what software I can use to infer phylogeny trees?

Thanks

Answer 1

[pld]

The file formats are listed in the Gblocks documentation

As for phylogenetic inference, you're asking a very large question. There are many programs that implement a very wide range of algorithms each having different and non-trivial theoretical underpinnings. You might want to start with a review such as this.

MrBayes, PhyML, PAUP*, MEGA, BEAST, etc. Some of these programs have different options for which algorithms, some are more up to date than others. There's also a decent amount of legwork to do ahead of time in selecting the model and setting any parameters the program requires.

[tony]

Hi Joe,

Thanks for the information. I was already familiar with MEGA and PAUP. I just wanted to know more programs that have different variations of algorithms for phylogenetic inference.

[pld]

I'd start with that review it explains the approaches and usually talks about one or two programs that implement them. For each of the methods in that review there are other reviews you can check that go into more detail.

MEGA and PAUP also implement different algorithms for phylogenetic inference. So if you're familiar with those programs you might want to try the different offerings they have first. Maybe MrBayes would be the next step after that.