FastTree: computing large minimum evolution trees with profiles instead of a distance matrix.
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix.
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DOI：
10.1093/molbev/msp077
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发表时间：
2009-07
影响因子：
10.7
通讯作者：
Arkin AP
中科院分区：
文献类型：
--
作者：
Price MN;Dehal PS;Arkin AP
基因家族正在迅速增长，但用于推断基因突变的标准方法不能扩展到超过10，000个序列的比对。我们提出了FastTree，一种方法，用于构建大的migrationenies和估计其可靠性。FastTree不存储距离矩阵，而是存储树中内部节点的序列配置文件。FastTree使用这些配置文件来实现Neighbor-Joining，并使用查询来快速识别候选连接。FastTree然后使用最近邻交换来减少树的长度。对于N个序列、L个位点和不同字符的比对，距离矩阵需要O（N2）空间和O（N2 L）时间，但FastTree只需要O（NLa + N）内存和O（Nlog（N）La）时间。为了估计树的可靠性，FastTree使用了局部自举，这在距离矩阵上又提供了100倍的加速。例如，FastTree在17小时和2.4 GB内存中计算了158，022个不同的16 S核糖体RNA的树和支持值。仅仅计算成对的Jukes-Cantor距离并存储它们，而不推断树或自举，将需要17 h和50 GB的内存。在模拟中，FastTree比Neighbor-Joining、BIONJ或FastME稍微准确一些;在真正的比对中，FastTree的拓扑结构有更高的可能性。FastTree可在http://microbesonline.org/fasttree上获得。
Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement Neighbor-Joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N2) space and O(N2L) time, but FastTree requires just O(NLa + N) memory and O(Nlog (N)La) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 h and 2.4 GB of memory. Just computing pairwise Jukes–Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 h and 50 GB of memory. In simulations, FastTree was slightly more accurate than Neighbor-Joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
TreeFam：动物基因家族系统发育树的精选数据库
影响因子：
14.9
作者：
Li, Heng;Coghlan, Avril;Ruan, Jue;Coin, Lachlan James;Heriche, Jean-Karim;Osmotherly, Lara;Li, Ruiqiang;Liu, Tao;Zhang, Zhang;Bolund, Lars;Wong, Gane Ka-Shu;Zheng, Weimou;Dehal, Paramvir;Wang, Jun;Durbin, Richard
通讯作者：
Durbin, Richard
影响因子：
1.7
作者：
Desper, R;Gascuel, O
通讯作者：
Gascuel, O
影响因子：
4.3
作者：
Engelhardt BE;Jordan MI;Muratore KE;Brenner SE
通讯作者：
Brenner SE