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z-~Z|xuD|?UEv>1|_zDJI^E2n%{z!Vk8azgF2Mh7E+)Ito9DAp+f4Wr5?D!1Q$Gm!rg>f(Y5=*69c*UybkVnvr}*q?+i?#xgLi0cFry?ru0dVYwKd2H}m1D3`vu z*aX1x?12I096hQcH{Ljqz}GC&Kl;($@HH>!U;nZH_O6$%Tetd!=~UvfNF>^h4}-<9 zL(YM8-@xEqsW(&>h(D9dS5AzN&J1nezIX6LAO8De$dfW^?G0~uMeWFu(cIHd?}O~$ z{M3u#Qj59MbE>1x0+q-$NCXjV3XQj|iKQ@`O+e&{)hZwip4rCL_CRGIFi;)Wk^t2W zaxZobq6d+EF&tU7=PWEQ76A}QEX!ECzh8xhhgG7RqKT*jzMI-oAZ*;jzc|Qlz1!49X63-~RSj*JnmErF(zy5Y-UX z)>c)`WSX67I**-XEWFR%PGjXyV+dnI1cYhOGMw)T2Ll%(H0|PN6aKtHc(ikYAuukM zF=d$!A`v(s0wR6*wXeN4-kD6szWKdfp{c1HIhe7GZ_)|^zvx9JlquIWVMvTe`X&Sc|!6NGcnZ{E{2a9HdH-v#48FZ~8M z7qfAuOuDp&5a=$pCXT6}L1b}p;>GosdxKmo=wIBq=Go-;`_ - Core-genome alignment and analysis +* `Gingr `_ - Interactive visualization of alignments, trees and variants +* `HarvestTools `_ - Archiving and postprocessing -================= -Overview -================= +**Citation (preprint)** -Harvest is a suite of core-genome alignment and visualization tools -for quickly analyzing thousands of intraspecific microbial -genomes. Harvest includes Parsnp, a fast core-genome multi-aligner, harvest-tools, a binary archive format and format conversion tool, -and Gingr, a dynamic visual platform. Combined they provide -rapid core-genome alignments, variant calls, recombination -detection, and phylogenetic trees. + Treangen TJ, Ondov BD, Koren S, Phillippy AM. + "Rapid Core-Genome Alignment and Visualization for Thousands of Microbial Genomes." + *bioRxiv* (2014). doi: http://dx.doi.org/10.1101/007351 -.. image:: example.png - :target: https://raw.githubusercontent.com/marbl/harvest/master/docs/example.png +**Download (v1.1, 6-Feb-2015)** -Contents: +* `Harvest-OSX64-v1.1.tar.gz `_ +* `Harvest-Linux64-v1.1.tar.gz `_ .. toctree:: - :maxdepth: 1 - :numbered: + :hidden: - content/hardware - content/installation content/gingr content/parsnp content/harvest-tools - content/faq -