I would like to use PopART software for creating haplotype network. When I tried to upload the alignment of 122 sequences by inserting blocks for traits and coordinates, the software gets stuck by showing uploading alignment 49%.
May I know what might be the reason?
Rahul
First you must convert the fasta file to sequential nexus file format through this link
https://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html
you can download the file
then open it with notepad
add at the end of the file the traits like this:
BEGIN TRAITS;
Dimensions NTRAITS=6;
Format labels=yes missing=? separator=Comma;
TraitLabels Rashid MarsaMatrouh Damietta Bahari Lake_of_Burullus Abokir;
Matrix
Dvuabk1-COI 8,4,3,8,6,10
Dvuabk12-COI 1,0,0,0,0,1
Dvuabk3-COI 0,0,0,0,0,1
Dvuabk7-COI 0,0,1,0,1,1
Dvuabk9-COI 1,2,0,0,0,1
Dvubb10-COI 1,0,0,2,1,0
Dvudm5-COI 0,0,1,0,0,0
Dvur13-COI 1,0,0,0,0,0
Dvur8-COI 1,0,0,0,1,0
Dvubb7-COI 0,0,0,0,1,0
;
end;
where:
Ntraits: is the number of locations you have
Then write the traitlabels as mentioned above
The matrix here
Are the haplotypes sequences (10 haplotype here) but its name must be as the inserted sequence of the fasta file (choose one of the sequences)
Then the numbers next related to (how many samples in each location have that haplotype sequence)
Where the arrangement must be as the arrangement of the trait label above
For example
Dvuabk1-COI 8,4,3,8,6,10
Means the sequence named Dvuabk1-COI (considered as haplotype) found in 8 samples of Rashid , 4 marsamatrouh, 3 Damietta, 8 bahari, 6 lake of burullus and 10 abokir.
After the file is ready
Open popart software::
File> open-all files > open the edited sequential nexus file.
Then choose the network you want and change its color if wanted
Aligned multifasta groups you should convert into Nexus file with MEGA. After you can do trait file. It is easy: use sequenses name and tab separeted colum as a trait coordinate.
There are many ways to do that. My favorite one is use DNAsp to generate a nexus file of haplotypes (less sequences, less chances to get stuck), also DNAsp check for non [ACTG] caracteres which is not accepted by PopArt. Then you will need a table of haplotype frequency, which you could get in Arlequin, because the DNAsp table is differently formatted. Than just open the nexus files and complete the traits manually. That's easy and you have sure about what you are uploading to the software. Have sure everything is tab formatted.
I hope it helps you.
First you must convert the fasta file to sequential nexus file format through this link
https://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html
you can download the file
then open it with notepad
add at the end of the file the traits like this:
BEGIN TRAITS;
Dimensions NTRAITS=6;
Format labels=yes missing=? separator=Comma;
TraitLabels Rashid MarsaMatrouh Damietta Bahari Lake_of_Burullus Abokir;
Matrix
Dvuabk1-COI 8,4,3,8,6,10
Dvuabk12-COI 1,0,0,0,0,1
Dvuabk3-COI 0,0,0,0,0,1
Dvuabk7-COI 0,0,1,0,1,1
Dvuabk9-COI 1,2,0,0,0,1
Dvubb10-COI 1,0,0,2,1,0
Dvudm5-COI 0,0,1,0,0,0
Dvur13-COI 1,0,0,0,0,0
Dvur8-COI 1,0,0,0,1,0
Dvubb7-COI 0,0,0,0,1,0
;
end;
where:
Ntraits: is the number of locations you have
Then write the traitlabels as mentioned above
The matrix here
Are the haplotypes sequences (10 haplotype here) but its name must be as the inserted sequence of the fasta file (choose one of the sequences)
Then the numbers next related to (how many samples in each location have that haplotype sequence)
Where the arrangement must be as the arrangement of the trait label above
For example
Dvuabk1-COI 8,4,3,8,6,10
Means the sequence named Dvuabk1-COI (considered as haplotype) found in 8 samples of Rashid , 4 marsamatrouh, 3 Damietta, 8 bahari, 6 lake of burullus and 10 abokir.
After the file is ready
Open popart software::
File> open-all files > open the edited sequential nexus file.
Then choose the network you want and change its color if wanted
Hi Engy T. Megahed , I would like to extend my gratitude, your instructions on how to create the network using PopArt were so helpful...I have been struggling for a while. You have made my day. Thanks
Dear Engy T. Megahed ,
I'm trying to add trait on my haplotype net work using Popart following the instructions you provided above, but I get confused on how to name the sequences in the Trait matrix, especially the number after the sequence name,
I tried one way, but I cant import the file in popart, as the software stop to function when I want to import the trait file.
Of course George Lohay , my brazilian friend Pedro Bragança helped me.
Thanks for your concern
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