DNA Local ALignment Search

There are two tools actually available on this site:

Local Alignment Search Tool: A tool for making searchs of local alignments of a DNA sequence in the reference genomes of different species.
Phylogenetic Tree Generator Tool: A tool for generating phylogenetic trees from a FASTA file containing a multiple alignment of DNA sequences.

These tools could be useful for evolution studies.

A way to use these tools is:

Get a known SINE sequence and find repetitions on the different genomes making use of the tool for searching local alignments. Retrieve FASTA files with the results.
Make a multiple alignment of all the sequences found. You can use a tool like Clustal Omega.
Make a phylogenetic tree from these sequences to observe the signals of the evolution of these repetitive sequences.

See some example results:

More examples of use:

List of homolog candidates in chromosome 7 of mouse for dog Apoe gene.
Ercc2 human gene homolog candidates in chromosome 19 of chimpanzee.
A sequence in the sapiens chromosome 7 (forward strand) with resemblance to human Shox gene despite not being its homolog.
Icam1 hamster gene homolog candidates in chromosome 9 of mouse.
Phylogenetic tree of Ebola virus strands.
Phylogenetic tree of 35 mammals.
Phylogenetic tree of some hominids based on mitochondrial DNA.
Phylogenetic tree of some modern humans based on a specific region.

Technical specifications

These tools make use of specific technologies developed for this site. These technologies may have some advantages and disadvantages over other technologies (see here). Some requirements to consider while using these tools are:

Local alignment search is actually slower than searches made with BLAST technology. It can take as long as an hour to make a search of a long gene in a single chromosome. In contrast, it finds alternative matches and these matches in general look more suited for phylogenetic studies given that only full length matches are returned.
Sensitivity level 1 is faster and usually enough unless you are looking for very distant homologs. Sensitivity level one with random selection of chunks is an even faster method and usually enough for not too distant homologs.
The phylogenetic tree generator is actually faster in general than similar softwares, making it possible to generate phylogenetic trees for hundreds of elements in a few minutes or even seconds. Despite that, once the number of elements exceeds one thousand, an exponential effect begins to manifest and the processing time starts growing exponentially. For that reason the number of elements per tree is actually limited to 1500.
The phylogenetic tree generator tool makes use of a bottom up strategy which seems to be well suited for large trees with abundant data. I usually find the trees to make more sense than trees generated with most alternative softwares, but maybe that's only my impression.
Given the limited resources for this project, the number of jobs you can queue is limited and some other parameters, like the length of the sequence, are also limited.
To reduce costs, and given that this project is actually an experiment, the servers processing job queues are only active a few hours per day. You can fill jobs at any time but the jobs will only be attended during the scheduled hours.