In this section, CottonFGD accepts users' input sequences, align them with MAFFT and build a simple phylogenetic tree using FastTree(v2.1) as the back-end program.

$ mafft --preservecase --reorder [input.fa] >[input.align.fa]
$ FastTree [input.align.fa] >[tree.nwk]

Choose Other Parameters

Phylogenetic tree buildding is a highly complex work requiring many parameters. If you want to choose other models/parameters/statistical methods, we recommend you to download the sequences in FASTA format and uses specific software (such as MEGA GUI) to do it.

CottonFGD uses the Phylo.io app to view trees. View its user manual to see the detailed help information.

Tools: Phylogenetic Tree Construction & View

Tree Construction

Choose Other Parameters

Tree View