Tools for alignments

@thermokarst Question for @SoilRotifer: Is there any online tool (external to QIIME) that you can recommend to quickly generate the alignments and / or phylogenetic trees? These steps generally take a long time on a regular laptop or desktop PC. Thanks. Juan

Hi @ju4n_dc,

There are many web services out there. Often you can use search terms like: RAxML web service

How many sequences are you trying to analyze? What gene and/or region are you aligning?
Have you checked-out the Phylogeny tutorial? Generally, mafft and fasttree are quite fast. In fact, you can run all the steps as one command: qiime phylogeny align-to-tree-mafft-fasttree …

Otherwise you can checkout these online services:



+1 for all of @SoilRotifer’s recommendations. I’m not sure if the other programs have an equivalent function, but I sure like the option with iqtree where you let it pick the optimal model, rather than trying to figure it out yourself.

1 Like