I would like to figure out the sequence conservation of some lncRNAs in different organisms (mouse, rat and human). I have already obtained the nucleotide sequence of the lncRNA gene (both introns and exons) in mice and its homolog in the rat and human genome. I have also tried to align the sequences ( 2 at a time) using the "Align Sequences Nucleotide BLAST" tool (http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=align2seq), which enabled me to see some similarity between the two sequences. Now I am looking for a way in which I can visualize better the homolog between the sequences a bit better so that I can maybe include it in my paper. Hence, I would like to make similar figures like figure 1 and 2 from the paper in the attachment. I tried to install the PHylogenetic Analysis with Space/Time models (PHAST) software package on my computer, but it looks very complicated to use and I have no clue as to how to use it to analyse my sequence conservation. Can anybody suggest me any (user-friendly) software I can use to analyse the sequence conservation and be able to generate figures like 1 and 2 from the attached paper? Alternatively, do you know any (easy) PHast guide/instructions?
http://genomebiology.com/content/11/7/R72
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