Five ways to import data into PhyloSuite

Posted on Edited on In

1. Search in the NCBI

Please see https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#4-3-3-1-Brief-example.

2. Download by IDs

When you are in the PhyloSuite root folder, go to example\GenBank_entries_display_and_extract folder, open 104_flatworms_mtDNA_IDs.txt file to copy the IDs.

  1. Open the window via file-->Import file(s) or ID(s) in the menu bar;
  2. Enter IDs;
  3. Enter your email to tell NCBI who is downloading the sequences;
  4. Select a work folder to deposit the sequences; selecting a work folder of GenBank_File category will download GenBank format sequence(s), selecting a work folder of Other_File category will download FASTA format sequence(s);
  5. Click Start.

3. Drag files to import

When you are in the PhyloSuite root folder, go to example\GenBank_entries_display_and_extract folder:

  1. Select a work folder in the GenBank_File root folder;
  2. Drag 21_flatworms_mtDNA.gb file and drop it in the display area.

You can also drag a fasta file: each sequence in the file will be converted automatically to the GenBank format. Go to example\Convert_format folder and then drag cox1_NUC_mafft.fas file to the display area. The sequence name will be used to automatically fill both ID and Organism columns.

Files with sequences in fasta, phylip and nexus formats, as well as sequences recorded in a Word document, can be drag-dropped into the work folder in Other_File root folder:

4. Use button to import

  1. Open Input window via file-->Import file(s) or ID(s) in the menu bar, then click Choose Files to open files;

  2. When a work folder is empty, you can click Open file(s)/Input ID(s) in the display area to open files.

  3. When there are sequences in the work folder, you can use Add file option, accessed via the right-click menu.

5. Copy to import

  1. Select a work folder in the GenBank_File root folder;

  2. Open 21_flatworms_mtDNA.gb file (see 3.3), CTRL+A to select all the contents, CTRL+C to copy, then CTRL+V to paste them in the display area.

  3. Similar to step 2, you can also open cox1_NUC_mafft.fas (see 3.3) file to copy its contents to the display area.

  4. When you have a raw sequence, you can also copy it into the work folder.

  5. Reversely, you can also select and copy (CTRL+C) sequences in the display area (the content will be copied to clipboard in the GenBank format).

Other demo tutorials can be seen here.