{"id":72,"date":"2022-01-12T09:51:56","date_gmt":"2022-01-12T09:51:56","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/research-beta\/goldman\/?page_id=72"},"modified":"2026-03-06T12:20:03","modified_gmt":"2026-03-06T12:20:03","slug":"software","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/research\/goldman\/software\/","title":{"rendered":"Software"},"content":{"rendered":"\n
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AIS<\/a><\/td>A<\/strong>lmost I<\/strong>nvariant S<\/strong>ets<\/td><\/tr>
ALVIS<\/a><\/td>Interactive non-aggregative multiple sequence AL<\/strong>ignment VIS<\/strong>ualisation – see also Sequence Bundles<\/a> below<\/td><\/tr>
AYB<\/a><\/td>Base calling software for the Illumina GA platform<\/td><\/tr>
BOSS-RUNS<\/a><\/td>B<\/strong>enefit-O<\/strong>ptimising S<\/strong>hort-term S<\/strong>trategy for R<\/strong>ead U<\/strong>ntil N<\/strong>anopore S<\/strong>equencing<\/td><\/tr>
EDIBLE<\/a><\/a><\/td>E<\/strong>xperimental D<\/strong>esign and I<\/strong>nformation B<\/strong>y Likelihood E<\/strong>xploration.<\/td><\/tr>
KAV<\/td>KA<\/strong>lignmentV<\/strong>iewer – an interface for the display and browsing of multiple sequence alignments – is no longer distributed or supported<\/td><\/tr>
MAPLE<\/a><\/td>MA<\/strong>ximum P<\/strong>arsimonius L<\/strong>ikelihood E<\/strong>stimation<\/td><\/tr>
PANDIT<\/a><\/td>PANDIT<\/strong> database of alignments and trees of P<\/strong>rotein and A<\/strong>ssociated N<\/strong>ucleotide D<\/strong>omains with I<\/strong>nferred T<\/strong>rees<\/td><\/tr>
PASSML<\/a><\/td>P<\/strong>hylogeny a<\/strong>nd S<\/strong>econdary S<\/strong>tructure using M<\/strong>aximum L<\/strong>ikelihood.<\/td><\/tr>
pcrcoal<\/a> <\/td>R package for coalescent simulations of PCR<\/td><\/tr>
PEAR<\/a><\/td>P<\/strong>hylogeny E<\/strong>mbedding & A<\/strong>pproximate R<\/strong>epresentation<\/td><\/tr>
phastSim<\/a><\/td>fast phylogenetic simulator<\/td><\/tr>
PhyloSim<\/a> <\/td>Monte Carlo simulation of sequence evolution<\/td><\/tr>
PRANK<\/a><\/td>P<\/strong>robabilistic A<\/strong>lignment K<\/strong>it<\/td><\/tr>
webPRANK<\/a><\/td>Web<\/strong> server for PRANK<\/strong> sequence alignment<\/td><\/tr>
RATS<\/a><\/td>R<\/strong>esource A<\/strong>ware T<\/strong>axon S<\/strong>election<\/td><\/tr>
rlsim<\/a><\/td>rlsim collection of tools for simulating RNA-seq<\/td><\/tr>
RNAcode<\/a><\/td>Analysis of protein coding potential in multiple sequence alignments<\/td><\/tr>
Sequence Bundles<\/a><\/td>interactive multiple sequence\u00a0alignment\u00a0visualisation<\/td><\/tr>
SLR<\/a><\/td>S<\/strong>itewise L<\/strong>ikehood R<\/strong>atio estimation of selection<\/td><\/tr>
simNGS<\/a><\/td>Sim<\/strong>ulating observations from Illumina NGS<\/strong> machines<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

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