Anyone know how to concatenate several gene sequences for phylogenetic analysis?

You can concatenate alignments using the Geneious soft. (http://www.geneious.com/)

https://support.geneious.com/entries/22610588-Combining-gene-regions

1) you can use an online Fasta alignment joiner tool to concatenate gene sequences: http://users-birc.au.dk/biopv/php/fabox/alignment_joiner.php; gene sequences have to be in fasta format and in the same order.

2) Align each data set separately before concatenate.

Jainder Chhillar

thanks eleonora, filipe and ortac i am going to try all options.

Atena Eslami

Hi, first of all try your best to assemble your data in FASTA format, then use different softwares such as bioedit, mesquite, cluslaw and etc.

MEGA5, GeneALEX and NTYsis are good softwared which help you to separate your samples phylogenetically.

Jainder Chhillar

thanks atena

Atena Eslami

YOUR WELCOME

Jainder Chhillar

thanks xavier i will try both

Rahul Arvind Jamdade

Here it is, Sequence Matrix:

Sequence Matrix (Vaidya et al., 2010) facilitates the assembly of phylogenetic data matrices with multiple genes. Files for individual genes are dragged and dropped into a window and the sequences are concatenated. A table provides an overview over how much sequence information is available for the different genes and species. The user can request Sequence Matrix generate a wide variety of character and taxon sets (e.g. a taxon set with all species that have more than a specified number of genes or basepairs). The concatenated sequences can be exported in NEXUS or TNT format. Individual sequences can be excluded from being exported.

(Download link for recent version of the above mentioned software: https://sequencematrix.googlecode.com/files/SequenceMatrix-Windows-1.7.8.zip)

Reference:

Vaidya, G., Lohman, D. J., Meier, R. (2010) SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics, early view.

(Dowload link for Reference: http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2010.00329.x/abstract;jsessionid=5828B885FAB6CE39ECBA4027CA4B22EA.f04t01)

Jainder Chhillar

thanks rahul for the suggestion but the above link for download is not working can i download it from some other place.

Rahul Arvind Jamdade

Ok, here is your download...

(Attachment: SequenceMatrix-Windows-1.7.8.zip)

Jainder Chhillar

thanks rahul, i will get back to you for any help regarding the software.

Jainder Chhillar

Respected Mr. Liu,

thanks for your reply, i too have been using Mega 6 and i need help regarding how to concatenate using mega or any other software. it is clear to me that number of taxa and no of sequences should be same for all the analysed markers. another thing i need help with is whether there is any software we can use to compare two phylogenetic trees also. with regards,

jai

André Levy

I have an associated question: say you have multiple markers for several species, and dor aome combination marker*species you have more than one sequence. What is the mosr correct way to prepare the concatenated matrix for a Bayesian analysis in Mr Bayea for instance (I think the answer might be different for max pars ou liklihood): would it be to have a single entry of that species with some polymorphic or ambiguous sites, or separate entries for variation? (I know that alternately one could use a BEST or *BEAST approach that estimates the best species topology given several estimates of geneologies. But I still am interested in the question above.)