Hi Pepijn, this is a bit of a late answer to this question - hopefully already solved. It is actually very easy to concatenate sequences in MEGA and there are several ways to achieve this. Probably the best is in the alignment editor. Make sure both sets of sequences have the same taxon composition and order. Then copy all from one set of sequences and simply paste it at the end of the others (place the cursor in the top cell at the end of the first sequence segment and paste all). I like to insert about 5 uncertain bases (?????) between the two segments so that I am sure where they end and start.

If two sequences (or set of sequences) are of same biological properties, the assumption is that they are evolving with similar rates. Therefore, its logical to concatenate them as well as their probable orthologs and paralogs (it depends what question your addressing with your trees) and than perform the analysis to get meaningful results.

Yes, I know that, but is it possible to do that with MEGA5?

Yes just 'copy-paste' the alignment of one gene on to the next one. Make sure the order of the samples is exactly the same in the two alignments.

Thanks, I'll try that :)

Geneious has a handy feature for that. Here the sequences don't need to be in the same order, but must have identical names. A big advantage is, that you can have different coverage of both markers (say sequencing failed for some of the samples for one marker). Geneious will figure out the association for you. I am not sure, though, if this feature is available in the free test version.

Hi Pepijn!! I don't want to mess you up more, but I would like to recommend you the software Mesquite, because is free (yuju!) and it has a very user-friendly alignment editor, in which you can easily concatenate molecular datasets (see Combining molecular matrices or sequences in the attached link). I hope you find it useful :)

Cheers!

S.

http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/molecular/molecular.html

Hi Pepijn, this is a bit of a late answer to this question - hopefully already solved. It is actually very easy to concatenate sequences in MEGA and there are several ways to achieve this. Probably the best is in the alignment editor. Make sure both sets of sequences have the same taxon composition and order. Then copy all from one set of sequences and simply paste it at the end of the others (place the cursor in the top cell at the end of the first sequence segment and paste all). I like to insert about 5 uncertain bases (?????) between the two segments so that I am sure where they end and start.

The question of whether the two fragments have conflicting evolutionary properties or histories is a good one but in practice, even when you can reject a consistent model, a concatenated model works well because the conflict is usually localised, with substantial agreement - and because you can contrast combined with single fragment analyses and see the strength and nature of conflict. I don't think it is necessary to consider the models as true evolutionary processes, just as adequate explanations of patterns of change. I see that Aparna already gave a similar answer to mine above.

regards

By using the software Gb2tnt. You only need to be sure that the species names are exactly the same in both datasets. Gb2tnt works even if you do not have sequences of both genes for all your species. The program will read your alignment or even the original sequences, then it will align them by using MUSCLE, after this it will create a block of each gene in a TNT file ready to be analized. The inputs are your files With sequences, which can be FASTA files or others.

you shoud firstly confirm that 2 gene sequence from the same individual, combine the two data sets you should using some software like Notepad and save txt file, finally, you can construct phylogenetic relationship tree with Mage software!

Thanks everyone for the useful answers! In the end I managed to get a license for Geneious, which is better in my opinion, because now I can analyze the chromatograms and align/concatenate everything in the same program.

Hi Pepijn, you could also try sequence matrix.

Hi there, What you are referring is a standard phylogenetic technique called "Concatenation". I've recently published a detailed, step-by-step concatenation protocol over at Nature Protocols https://www.researchgate.net/publication/248398863_Sequence_Similarity_Search_Multiple_Sequence_Alignment_Model_Selection_Distance_Matrix_and_Phylogeny_Reconstruction

Article Sequence Similarity Search, Multiple Sequence Alignment, Mod...

Interesting discussion. I would like to know how to assemble sequences that are overlapping. I am sequencing cytb gene and we sequence it in parts. I would like to know how to do it in Geneious and MEGA.