<html xmlns="http://www.w3.org/1999/xhtml" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office"><head><!--[if gte mso 9]><xml><o:OfficeDocumentSettings><o:AllowPNG/><o:PixelsPerInch>96</o:PixelsPerInch></o:OfficeDocumentSettings></xml><![endif]--></head><body><div style="color:#000; background-color:#fff; font-family:Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10px"><div id="yui_3_16_0_ym19_1_1520778559030_2739" dir="ltr">Dear all,</div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_2991"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_2947">For my work I needed a fast pairwise sequence aligner with more fine-grained control over gap penalties.</div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_2955">I have implemented a C extension to do this, which is available in this branch on github:</div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_2977"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3057"><a href="https://github.com/mdehoon/biopython/tree/pairwise_aligner" id="yui_3_16_0_ym19_1_1520778559030_3301">https://github.com/mdehoon/biopython/tree/pairwise_aligner</a></div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3056"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3055">There is some rudimentary documentation in Doc/Tutorial/chapter_align.tex (under section 6.5).</div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3205">Examples can be found in Tests/test_pairwise_aligner.py.<br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3217"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3182">I think this aligner can be a replacement for pairwise2 aligner.</div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3133">In particular, it is more flexible and more Pythonic, using a PairwiseAligner object to store the alignment scoring scheme instead of interpreting the function name (as in pairwise2).</div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3173"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3200">Comments are welcome.</div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3228">Note that this aligner returns PairwiseAlignment objects; it may be better to integrate this with the existing MultipleSeqAlignment class in Bio/Align.<br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3257"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3219"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3263">Best,</div><div dir="ltr" id="yui_3_16_0_ym19_1_1520778559030_3284">-Michiel<br></div><div id="yui_3_16_0_ym19_1_1520778559030_2824"><br></div><div id="yui_3_16_0_ym19_1_1520778559030_2933"><br></div></div></body></html>