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Based on Phylogenetic analysis of sequences from these 10 phytoplasmas using PAUP (phylogenetic analysis using parsimony) software, these phytoplasmas could be classified into five groups. These phytoplasmas groups and strains were: group 1, sweetpotato witches' broom, mainland China strain of sweetpotato witches' broom, peanut witches' broom and Ipomoea obscura witches' broom; group 2, loofah witches' broom; group 3, elm yellows; group 4, rice yellow dwarf and sugarcane white leaf disease; group 5, New Jersey strain of aster yellows and western strain of aster yellows.

从spacer序列堆衍的亲缘演化树显示这10种植物菌质体可分为5群：第一群，甘薯簇叶病、甘薯簇叶病、花生簇叶病及细花牵牛簇叶病等菌质体；第二群，丝瓜簇叶病菌质体；第三群，榆树黄化病菌质体；第四群，水稻黄萎病及甘蔗白叶病菌质体；第五群，翠菊黄化病菌质体。

Were analyzed phylogenetically by use of PAUP 4.0 software.

各组在分歧以后沿着各自的方向演化。

Optimal trees were inferred using PAUP based on second codon partition data and using MrBayes based on combined codon data, which showed good consistency and were consistent with the trees inferred from corresponding translated amino acid data.

此外，用对应的氨基酸序列生成的ME和MP树与第二密码子数据模块分析的结果也一致。

Mfold was developed to predict secondary structure of RNA. miRanda, TargetScan, PictTar and RNAhybrid are used for predicting miRNA's target gene. Amibion, Invivoge and Whitehead offer the function of siRNA design. PHYLIP, MEGA, PAUP* are famous software for analysis of phylogenetics. In addition, we discussed the bioinformatic works we need do in near future, i.e.

本文最后分析了目前非编码RNA网络资源存在的问题和不足，并展望了未来的研究方向，指出开发非编码RNA的跨库搜索引擎，序列和结构信息的二次挖掘软件，以及具有科学实证基础的二级结构预测软件将是未来该领域研究的重点内容。

By employing two kinds of molecular marker of mitochondrial DNA, i. e. Cyt b and CoI gene, the sequences of 15 species representing 6 families from Passeriformes were compared. We analysed their sequences compose and characteristic with the sorft of MEG3.1, and built the phylogenetic trees in PAUP~*4.0. We deeply analysed the feasibility that CoI gene qua the marker to research the phylogenetic relationship of Passeriformes, and afford the academic proof for building the DNA barcoding of the birds.

本文分别以线粒体DNA的细胞色素b和CoI基因作为分子标记，对雀形目6科15种鸟类的细胞色素b基因全序列(1，143bp)和CoI基因部分序列(1，176bp)的组成特点及其系统发育树进行了比较分析，还探讨了CoI基因作为雀形目系统发育研究和构建鸟类物种DNA编码库的分子标记的可行性，旨在为DNA编码库的构建积累基础资料。

Similar tree topologies were recovered by both MP and ML trees generated based on unweighted analysis using PAUP*. The Eublepharidae and Gekkonidae were monophyletic.

构建的MP树和ML树有相同的拓扑结构，提示睑虎科和壁虎科都是单系的，刺尾虎亚科+具攀瓣的絮趾虎类与鳞脚虎类+无攀瓣的絮趾虎类为姐妹群关系。

Finally,the WISCONSIN Sequence Analysis Package (GCG,10.2 version),Phylogenetic Analysis Using Parsimony (PAUP,4.0 version) and Treeview (1.5 version) software were used for data analysis,sequence translation,phylogenetic tree drawing and molecular evolution analysis.

本研究结果证明，H9N2亚型人体分离株属于G1-like亚分支的G1-HK小分支，该小分支毒株之间具有很高的同源性，因此该小分支AIV可能具有感染人的可能性，是具有引起人流感暴发潜能的病毒。

On the base of the constructing phylogenetic tree using PAUP 4.0, MP and NJ (neighbor-joining) trees of diverse pectate and pectin lyases showed that pectate lyases from plant, pectin lyases from fungi and pectate lyases from bateria belong to different groups, respectively. The pectate lyase A of Aspergillus nidulans is more closely related to plant pectate lyases than to pectin lyase from fungi and pectate lyases from bacteria. The pectin lyase from Pseudomonas syringae is more closely related to fungi pectin lyases than other lyases.

构建的MP树和NJ树(neighbor-joining)显示：来自植物的果胶酸裂解酶、真菌的果胶酸酯裂解酶、细菌的果胶酸裂解酶分别可聚为一个独立的类群；相对于细菌果胶酸裂解酶和真菌果胶酸酯裂解酶而言，构巢曲霉的果胶酸裂解酶A和植物的果胶酸裂解酶之间有较近的亲缘关系；细菌Pseudomonas syringae的果胶酸酯裂解酶和真菌的果胶酸酯裂解酶之间的亲缘关系较近。

The evolutionary relationships were investgated by comparing the results from molecular data alone or molecular data combined morphological characters using different analysis methods: maximum parsimony by PAUP(superscript *) 4.0 and Bayesian inference by MrBayes 3.0B4. Base composition and ti/tv of 28S rDNA D2 regions were analyzed by PAUP(superscript *) 4.0. The results showed that GC content of the 28S rDNA D2 gene sequences of subfamily Euphorinae ranges from 40.00% to 49.25%. Transversion frequency of sequence variable sites among species of Euphorinae was higher than that of transition. The subfamily Euphorinae was proved to be a paraphyletic group with close relationship to subfamilies Neoneurinae and Cenocoelinae; only two tribes, Meterorini and Microctonini, were proved to be monophyletic groups; Centistini, Cosmophorini, Euphorini and Dinocampini were paraphyletic groups; the basal position of tribe Meterorini within Euphorinae was partially supported by our phylogenetic trees, and tribe Microctonini was proved to be a group at the top of the trees.

结果表明：优茧蜂亚科的28S rDNA D2基因序列片段的GC%含量在40.00%~49.25%之间变动，而对于碱基替代情况来讲，优茧蜂亚科各个成员间序列变异位点上颠换大于转换；不同的分析和算法所产生的系统发育树都表明目前根据形态定义出的优茧蜂亚科Euphorinae不是一个单系群，而是一个与蚁茧蜂亚科Neoneurinae和高腹茧蜂亚科Cenocoelinae混杂在一起的并系群；在优茧蜂亚科内部，悬茧蜂族Meterorini和食甲茧蜂族Microctonini（排除猎户茧蜂属Orionis）为单系群，而宽鞘茧蜂族Centistini、大颚茧蜂族Cosmophorini、优茧蜂族Euphorini、瓢虫茧蜂族Dinocampini为并系群；悬茧蜂族Meterorini在优茧蜂亚科Euphorinae内位于基部位置的观点得到部分的支持，同时食甲茧蜂族Microctonini被判定为相对进化的类群。

Codon partition schemes were compared in phylogenetic analyses at subfamily level for Gyrinidae and at family level for Hydradephaga based on partial mitochondrial COⅠ gene sequences.

利用PAUP和MrBayes软件，对线粒体COⅠ基因序列3个密码子位置的数据模块分别进行了豉甲科和水生肉食亚目在亚科或科水平上的系统发育学分析，结果表明第二密码子数据模块获得了理想的分析结果。

For a big chunk of credit-card losses; the number of filings (and thus charge-off rates) would be rising again, whether

年美国个人破产法的一个改动使得破产登记急速下降，而后引起了信用卡大规模的亏损。

Eph. 4:23 And that you be renewed in the spirit of your mind

弗四23 而在你们心思的灵里得以更新