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USEARCH19DB editingFASTA universal and simple!, but non unifiedNCBI:>gi|269120277|ref|YP_003308454.1| carbamate kinase MKNRIVVALGGNALGNSAKEQRDAVRETAIPIVDLIEAGHEVILAHGNGPQVGMINLAMDSATKNLPSFAEMPITECVAMSQGYIGYHLQRFIRDELKRRNIDKEVATIVTEVLVDGDDPAFKSPNKPIGAFYTKEEAEKLEKQGYTMMEDAGRGYRRVVASPKPVDIVQKKTIKTLIDNSQIVITVGGGGIPVKYVEGKGTLGEFAVIDKDFASAKLAELIDADYLIILTAVEKIAINYGKENEQWLDKLSIDDAKKYIKEGHFAPGSMLPKVEAALGFAASKQGRRALVTSLEKAKDGIAGLTGTVIVDEK MGFlots of redundancy in dbs (duplicates, close paralogues.)usually it is better to get rid of themsequence clustering+ - speed, relative HW friendly, accuracy L/HGTpossible source of error: - sins of the pastĮGTLEUCA.ANIMALS/FUNGIPLANTSRHODOPHYTESEGT.18(16)S rRNA combination of variable and conserved regionszero L/HGTexhaustive taxon samplingknown secondary structurehundreds of copies per cell - single-cell PCRcost per nt + speed18S is always right+-~1800bpintraindividual paralogueslower branching supportMULTI-PROTEIN DATASETs+large ammount of informationmodularrobust branching support (although often false)-limited samplingvariable quality of phylohenetic signalL/H(E)GTstill costly and slowHW demanding analysisstability of topologies (or lack of thereof)
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OCTATCpossible source of error: - paraloguespossible source of error: - sins of the past but sometimes it doesntpossible source of error: - incorrect sequence annotation and sometimes it really worksĪdl et al, 2012. PhylogenomicsPhylogeneticsPhylogenomicsreconstruction of phyletic relationships based on the analysis of - several (to several dozens) genes- complete genetic information (ideal)- several dozens to hundreds of coding sequences (phylotranscriptomics)Why?vast amount of genetic information should significantly improve the prediction of phylogenetic relationships and eliminate signal noise.