MUSCLE run mode Click here for details.:

Note: parameters are adjusted according to the selected running mode

Maximum number of iterationsYou can control the number of iterations that MUSCLE does. If you specify 1, 2 or 3, then this is exactly the number of iterations that will be performed. If the value is greater than 3, then MUSCLE will continue up to the maximum you specify or until convergence is reached, which ever happens sooner. The default is 16. If you have a large number of sequences, curation may be rather slow.: (default: 16)
Find diagonalsCreating a pair-wise alignment by dynamic programming requires computing an L1 × L2 matrix, where L1 and L2 are the sequence lengths. A trick used in algorithms such as BLAST is to reduce the size of this matrix by using fast methods to find diagonals, i.e. short regions of high similarity between the two sequences. This speeds up the algorithm at the expense of some reduction in accuracy. MUSCLE uses a technique called k-mer extension to find diagonals. (faster for similar sequences)

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TNT Personal Use License (PUL) The TNT PUL allows you to use TNT free of charge for personal use only. If you do not belong to this category, you will have to purchase a commercial license. Do not hesitate to contact the authors of the program in this matter. If you are confused by the legalese to follow, you may also want to take a look at our Licensing FAQ (at www.zmuc.dk/public/phylogeny) to answer a few common questions. TNT PUL terms and conditions Version 1.1, May, 2008 The Authors grant you the right to use the software product as defined in § 1 according to the following provisions. If you do not agree to all conditions set forth by this license, you may not use the product, because only The Authors as the product's owners can give you permission to use it. The PUL allows you to download the TNT binaries for personal use, but it does not give you the right to redistribute these binaries. So you may not put them onto your own websites or other mirrors. § 1 Subject of license. "Product", as referred to in this License, shall be the binary software package "TNT", which allows for calculating and evaluating phylogenetic trees. The Product consists of executable files in machine code for the Windows 2000/XP, Linux and Mac operating systems as well as other data files as required by the executable files at run-time and documentation in electronic form. "The Authors", as referred to in this License, shall be Pablo A. Goloboff (who can be contacted at pablogolo@csnat.unt.edu.ar), James S. Farris (who can be contacted at msl-farr@nrm.se), and Kevin C. Nixon (who can be contacted at kcn2@cornell.edu § 2 Grant of license. The Authors grant you a personal right to install and execute the Product on a Host Computer for Personal Use or Educational Use. "Personal Use" requires that you use the product on the same Host Computer where you installed it yourself and that no more than one client connect to that Host Computer at a time for the purpose of running a phylogenetic analysis. § 3 Reservation of rights. Any use beyond the provisions of § 1 is prohibited. The Authors reserve all copyrights and other intellectual property rights. This includes, but is not limited to, the right to modify, make available or public, rent out, lease, lend or otherwise distribute the Product. This does not apply as far as applicable law may require it or The Authors grant you additional rights of use in a separate license in writing. § 4 Termination. This License shall be valid indefinitely. The Authors may terminate the License only for material causes. In particular, such a material cause can be a violation of the usage terms or a breach of other essential duties from this contract. After termina_ tion, you are required to delete and destroy all remaining copies of the Product. This includes, but is not limited to, installed copies and backups. § 5 No warranties. Since you have not paid for the use of the Product, there is no warranty for it, to the extent permitted by applicable law. The Authors provide the Product "as is" without warranty of any kind, either expressed or implied, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. The entire risk as to the quality and performance of the Product is with you. Should it prove defective, you assume the cost of all necessary servicing, repair, or correction. § 6 Publication of results. You are free to publish in a scientific journal any results derived from use of the program. In such a case, you have to (1) acknowledge that the program is being made available with the sponsorship of the Willi Hennig Society, and (2) cite the paper describing the program, published in "Cladistics, The Interna_ tional Journal of the Willi Hennig Society" (citation). § 7 Miscellaneous. There are no license terms beyond the written ones in this agreement. Amendments of, additions to and the joint revocation of this agreement shall require the written form. The same shall apply to the preceding written form requirement. Standard business conditions of the parties shall not apply. Place of performance and legal venue shall be San Miguel de Tucuman, the domicile of Pablo A. Goloboff. Solely Argentinian law shall apply to this agreement.

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Search type:

CostsNote: you can set the costs for both amino-acids and nucleic acids but only the appropriate one according to your data will be used.:

Resampling:

Tree can be customized using the dynamic tree editing interface.