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请教系统发育树分析过程中的问题
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刚做这方面的实验，我是小白菜，请大家指教！ 问题有点多，先答谢10个金币吧  1。由于样品基因片段比较短，有几个结果不确定，想通过构建系统发育树来分析一下，不知这样必要不？可行不？ 2。软件的选择：不知道有什么讲究吗？或者哪些更权威？我暂时打算用phylip，行不？ 3。ncbi的分析结果中，有Lineage Report ，Organism Report ，Taxonomy Report ，三者有何区别？另外，下面表hit值反映了什么（如Bacteria:表示50个结果隶属于这一大类，且是属于15种org？）？取舍的原则是什么（会不会因为某结果hit数最高而即使该菌在相关研究中未报到过或跟研究相关较小也选择它呢）？ -------------------------------------------------------------------------------- Taxonomy Report Bacteria .............................................. 50 hits 15 orgs [root; cellular organisms] . environmental samples ............................... 34 hits 3 orgs . . uncultured bacterium .............................. 32 hits 1 orgs . . uncultured eubacterium env.OPS 17 ................. 1 hits 1 orgs . . unidentified bacterium ............................ 1 hits 1 orgs . Bacteroidetes ....................................... 3 hits 3 orgs [Bacteroidetes/Chlorobi group] . . environmental samples ............................. 2 hits 2 orgs . . . unidentified Cytophagales OPB73 ................. 1 hits 1 orgs . . . uncultured Bacteroidetes bacterium .............. 1 hits 1 orgs . . Parapedobacter sp. 4M40 ........................... 1 hits 1 orgs [Sphingobacteria; Sphingobacteriales; Sphingobacteriaceae; Parapedobacter] . Proteobacteria ...................................... 13 hits 9 orgs . . Betaproteobacteria ................................ 12 hits 8 orgs . . . uncultured beta proteobacterium ................. 2 hits 1 orgs [environmental samples] . . . Burkholderiales ................................. 8 hits 5 orgs . . . . uncultured Herbaspirillum sp. ................. 1 hits 1 orgs [Oxalobacteraceae; Herbaspirillum; environmental samples] . . . . Burkholderiales Genera incertae sedis ......... 6 hits 3 orgs [unclassified Burkholderiales] . . . . . uncultured Aquabacterium sp. ................ 2 hits 1 orgs [Aquabacterium; environmental samples] . . . . . uncultured Rubrivivax sp. ................... 1 hits 1 orgs [Rubrivivax; environmental samples] . . . . . uncultured Ideonella sp. .................... 3 hits 1 orgs [Ideonella; environmental samples] . . . . uncultured Azohydromonas sp. .................. 1 hits 1 orgs [Alcaligenaceae; Azohydromonas; environmental samples] . . . unclassified Betaproteobacteria (miscellaneous) . 2 hits 2 orgs [unclassified Betaproteobacteria] . . . . beta proteobacterium BAC126 ................... 1 hits 1 orgs . . . . beta proteobacterium LF4-45 ................... 1 hits 1 orgs . . uncultured proteobacterium ........................ 1 hits 1 orgs [environmental samples] [ Last edited by shinyjoy on 2009-4-17 at 01:25 ] |
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