phylogeny using 2 alleles per loci data

Hello everyone,

I want to construct a phylogeny based on fasta sequences. Two sequences which contain two alleles stand for one individual, for example:

>indi_1_allele1
AATTCGC
>indi_1_allele2
ACTTAGC
>indi_2_allele1
ACGTAGC
>indi_2_allele2
ACGTATA
..

Does anyone know how to construct a phylogeny using these kind of data? What software can I use?

alignment phylogeny

• 1,455 views • link

updated 3.8 years ago by Ram

• written 11.0 years ago by Cherry •

1 answer

Do you have just one gene? If so, just add the two alleles as:

>sp1
sequence
>sp2_seq1
sequence
>sp2_seq2
sequence
>sp3
sequence
..

You may use any phylogeny recontruction software, such as PhyML, RAxML, PHYLIP, Mega...

• 0 views • link

updated 3.8 years ago by Ram

• written 11.0 years ago by h.mon

More posts like this

RNA-seq alignment in UNIX
written 4.3 years ago by Hien •

Hello everyone I am newer in bioinformatics. I would like to ask for your advice, helps, or comments on RNA-seq analysis in the class. Question: …
Error: Duplicate seq_ids are found
written 4.5 years ago by rupjandu •

Hello everyone, I am using the web-based Galaxy tool, not the command line version. I merged FASTA files into one and I'm trying to construct …
protein K-mer connection
written 8.3 years ago by kartik.aier.gta •

Hello everyone, I came across a problem in my work and would be grateful if anyone can help me out. The problem is stated below …
How to get nucleotide sequence from BAM file
written 9.2 years ago by davonairos •

Hi everyone! I apologize in advance for my ignorance. I'm just beginning in in a new bioinformatics project. I have a BAM file generated from …
Downloading sequences of genes related to a pathway in PlantCyc (or other cyc related databases) an…
written 10.5 years ago by ahmad.iut

Hello all, I am working on my RNA-seq data of a non-model plant and I want to find genes involved in a metabolic pathway. I …
How to concatenate gene sequence?
written 10.7 years ago by buthercup_ch •

Hello, With the aim of doing some phylogenetics based on Multi Locus Sequence Alignment, I need to generate concatenated sequences of several genes. Does anyone …
why does Pfam-A.fasta not contain all the sequences of a family?
written 11.0 years ago by ifishlin324 •

Hello everyone, I'm working on collecting sequences of each pfam family. And I realize **Pfam-A.fasta** (ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam28.0/relnotes.txt) consists of sequences in fasta format with PFAM accession, …
Sequence extraction from PFAM db with accession ID
written 11.4 years ago by venu

Hello, I have downloaded the local pfam data base from ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release. There are two databases **1) Pfam-A.fasta.gz 2) Pfam-A.full.gz** . The first one consist of …
Fasta Sequence For Each Hla Alleles
written 12.4 years ago by J.F.Jiang

Hi all, Since it is a new question for HLA typing, I post this question as new. After trying several public tools, such as HLAminer …
Phylogeny Study Based On Whole Genome Sequences
written 14.1 years ago by GAO Yang

Hi, everyone~ I got a denovo assembly genome of one kind fish. And now I want to do some evolution analysis, in particular, construct phylogeny …