Introduction :The main feature of this module is that it can help users explore the evolutionary relationships between uploaded gene sequences and homologous genes in the FishCODE database. Additionally, users can also independently perform evolutionary analysis on their uploaded sequences.
Steps : The first step is to upload/paste the protein sequence file in FASTA format. Step 2, Select the protein model for FastTree evolutionary analysis. If the user needs to combine the gene with the homologous gene of the corresponding 35 species of fish for evolutionary analysis, they can select the corresponding option. 3. In the third step, click the “Submit” button, and the visualization of the corresponding evolutionary tree analysis will be available in about 4~5 minutes. for details, please see "Genome analysis" section in Help Module
Dependent software : Sequence alignment (muscle 5.1.linux64), evolutionary analysis (FastTree 2.1.11), evolutionary tree visualization (ggtree 3.6.2), search for fish homologous genes in the FishCODE collection (diamond v2.0.15.153).
1. [Required] Paste the file which like fasta file: Note: only supports fasta type file as in the example file. Please note that when entering multiple protein sequences, sequence names(>XXXXX) are not allowed to be repeated |
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1. [ Required ] : Note: only supports fasta type file as in the example file, and does not support unicode type files. |
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2. Main parameters:
This module uses FastTree to build an evolutionary tree, please select the corresponding protein models:
Combine the user's gene with the homologous gene of the corresponding 35 species of fish for evolutionary analysis: