I think you should first assemble your sequences in fasta format and then align them. I use MEGA for Clustal and also you can use BIOEDIT software.

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.

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

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.

thanks atena

YOUR WELCOME

thanks xavier i will try both

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)

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

Ok, here is your download...

(Attachment: SequenceMatrix-Windows-1.7.8.zip)

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

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

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.)

SEAVIEW is a free software that displays a function to concatenate DNA sequences

@Kwasi Adusei-Fosu: It seems not compatible with Windows 10. I tried several times but it did not work. It works well on Mac. 

You can use Emboss( Union) available online and working on Linux

how to concatenate to genes phylogenetic trees?

yes...

the software SEAVIEW concatenates fasta files 

Hello, How does SEAVIEW concatenates fasta files? Wich tools need to be used?

Thanks!!

Mesquite is an option.

Check this video qhere explain how concatenate https://www.youtube.com/watch?v=unZ48A60yfs

You can concatenate your aligned sequences using GENEIOUS software. It’s user friendly.

Geneious software is OK and easy to use.

Geneious is OK and easy to use.

A simple tool for this:

https://github.com/nylander/catfasta2phyml

Can produce fasta or phyml outputs.

The question is 5-year-old however I want to add an answer for new searchers.

MegaX (the latest version) can be used for generate concatenated sequences. It's free of charge and easy to use.

Thank you sir for your kind information

whether to concatenate aligned sequences or unaligned fasta file in Geneious software for phylogeny

you can use AMAS, a python based nice tool for this purpose. It is easy and can handle any number of genes.

Genius prime can also be used

thank you, sir this is free software ?