1.

Write all the Accession Numbers of all the sequences that we want to include
 Format .txt
 List in vertical form
2. Sort by sequence length in the website
3. Send to:
a. Complete record
b. File
c. Format accession list
d. Sort by: sequence length
e. Create file
4. Also from our AliView (to open Fasta files), or any other text software:
5. Copy the sequence and paste in BLAST
a. All sequences that are most similar, appear first
b. Select some
c. Download as table (.csv)
d. Copy accession numbers and paste in the main file of accession numbers

6. GenBank Batch
a. Upload the file with accession numbers
b. Send to: format: FASTA
7. Add my own sequence in the FASTA file
a. Change the name appropriately

IN MEGA SOFTWARE
8. Align > Edit/Build alignment > DNA
9. Open our fasta File
10. Alignment > alignment by muscle
11. Select all? Ok
12. Default settings > OK

13. Data > export Mega alignment > MEGA format

14. Protein coding? NO  because it’s full genome
a. .meg
15. Models > find the best DNA/Prot model
16. Open the .meg file
17. It Gives a table (if not shown, export as excel file
18. Phylogeny > maximum likelihood tree
19. Test of phylogeny > bootstrap method
a. At least 100
20. Select the best model from the last step
21. Export current tree: .nwk

22. In FigTree  Import the tree file and play around to make it nicer
23. We need to show the accession numbers and any other relevant name.