Newbie at odds with large alignment

[MikeT]

Greetings everybody,
I'm new to the world of sequencing, and I'm trying to develop a metagenomic project for my university.
We had some viral DNA sequenced with 454; I assembled it following the parameters given in some papers on the topic and tried to assess the relationship of my contigs to real viral DNA sequences. So I aligned some selected contigs to published sequences using the server side of MAFFT and then downloaded the very large file that came along with it (roughly 1 GB, ClustalW format).
Now I'd like to build a tree with this data, but I'm reporting some issues, since almost all the programs I tried to use (UGENE, CLC Sequence Viewer, Geneious, ClustalX...) tend to crash on my laptop (a 2,2 GHz MacBook Pro with 4 GB of RAM). The only two programs that managed to work with the file were MAFFT and ClustalW, but they take a huge amount of time to elaborate it.
Since I don't think I can leave the laptop working on it forever and I have no access to more powerful workstations, is there any way to speed up the process?
Thank you for your answer.

Michael Tangherlini

[KevinLam]

I would have to ask why are you building a tree?
are u trying to identify the virus you have sequenced?

[MikeT]

No, I'd just like to see if there are any group similarities between the contigs I assembled and known viral genomes. I managed to extract a rough UPGMA tree for my alignment using ClustalW, but I'd like to get a more refined tree.
I have a total of 1914 sequences, lengths ranging from 1Kb to 100Kb.

-MikeT

[colindaven]

Hi Mike,

why don't you try the following.

Use Mummer/BLAST/newbler/BWA against all viruses.

See which have the most hits / matches.

I don't think you'll have much joy with trees and this amount of data. However the fastest alignment program I came across is muscle. That worked for large amounts of data for me in the past.

Colin