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If you want to restore a set number of bases on either or both ends of your trimmed sequences because your trim was too stringent or you want to improve coverage, Batch Revert Trim Ends lets you do that. With a few clicks, you can restore bases to a few or a few thousand sequences, and get even more control over your sequence trims.
Apply Sequencher's versatile assembly tools to
MUSCLE
MUSCLE[2], a multiple-sequence alignment (MSA) program, joins the Sequencher 5.1 family of plugins. It joins Clustal, making it the second MSA program in Sequencher’s DNA-Seq Tools. Boasting both speed and accuracy, it compares very favorably [3] to other multiple-sequence alignment programs.
MUSCLE is said to have four major steps in its alignment process. The first step constructs a distance matrix between pairs of sequences using k-mer clustering, this is then converted into a tree. The second step uses this tree to guide a progressive alignment. In the final two steps, the MUSCLE algorithm tries a number of different methods to see if it is possible to improve the tree and hence the multiple alignment.
Once the process is complete and MUSCLE has built the alignment, you will see the results as a contig within Sequencher. Use Sequencher’s tools to annotate your alignment or export your alignment and place it into a special phylogenetics program.
Sequencher DNA序列分析软件是科学家们*的工具。持续发展和改进**过25年,Sequencher提供了**的功能特征,成千上万的出版物都有相关的应用介绍。新手用户可以以少的时间投资产生结果,而有经验的用户会惊叹于功能的深度和控制。Sequencher自带各种专有算法,可以为Sanger, Next-Gen Sequencing (NGS)和RNA-Seq序列数据生成结果。
Sequencher 5.4.6新功能
为DNA序列分析提供了全新的和增强的功能。
Sanger
Sequencher Connections中运行的 Primer-BLAST发送引物序列到您的Sequencher项目中。
在项目窗口中轻松使用一致性序列,作为NGS测序比对混合的参考序列。
新批量处理恢复结束命令。
在项目窗口中调整字体大小的功能。
NGS
GSNAP和BWA-MEM工作流更快。
构建GSNAP数据库和BWA索引,这些索引可以被重新用于与整个基因组的对齐。
查看并保存用FastQC报告的NGS原始数据文件的质量分数和元数据。
使用SAMtools在您的NGS校准中标记变量来生成不同的调用文件(VCF)。
RNA-Seq
随着Cuffquant和Cuffnorm的添加,扩展了Cufflinks套件的功能。
Cuffdiff和 Cuffnorm的Conditions and Replicates编辑器。
使用自定义排序和筛选选项来增强RNA-Seq可视化功能。
使用增强的外部数据浏览器轻松管理所有的DNA-Seq和RNA-Seq项目。
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