HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing
Abstract Background Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with d...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2017-09-01
|
| Series: | Algorithms for Molecular Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13015-017-0116-x |
| _version_ | 1818175755585060864 |
|---|---|
| author | Shixiang Wan Quan Zou |
| author_facet | Shixiang Wan Quan Zou |
| author_sort | Shixiang Wan |
| collection | DOAJ |
| description | Abstract Background Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types. Methods Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction. Results The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource. Conclusions THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign . |
| first_indexed | 2024-12-11T20:05:20Z |
| format | Article |
| id | doaj.art-00d32558291f436fac10fb601dbde0e1 |
| institution | Directory Open Access Journal |
| issn | 1748-7188 |
| language | English |
| last_indexed | 2024-12-11T20:05:20Z |
| publishDate | 2017-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Algorithms for Molecular Biology |
| spelling | doaj.art-00d32558291f436fac10fb601dbde0e12022-12-22T00:52:24ZengBMCAlgorithms for Molecular Biology1748-71882017-09-0112111010.1186/s13015-017-0116-xHAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computingShixiang Wan0Quan Zou1School of Computer Science and Technology, Tianjin UniversitySchool of Computer Science and Technology, Tianjin UniversityAbstract Background Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types. Methods Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction. Results The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource. Conclusions THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign .http://link.springer.com/article/10.1186/s13015-017-0116-xMultiple sequence alignmentPhylogenetic treesDistributed computingSpark |
| spellingShingle | Shixiang Wan Quan Zou HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing Algorithms for Molecular Biology Multiple sequence alignment Phylogenetic trees Distributed computing Spark |
| title | HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing |
| title_full | HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing |
| title_fullStr | HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing |
| title_full_unstemmed | HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing |
| title_short | HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing |
| title_sort | halign ii efficient ultra large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing |
| topic | Multiple sequence alignment Phylogenetic trees Distributed computing Spark |
| url | http://link.springer.com/article/10.1186/s13015-017-0116-x |
| work_keys_str_mv | AT shixiangwan haligniiefficientultralargemultiplesequencealignmentandphylogenetictreereconstructionwithdistributedandparallelcomputing AT quanzou haligniiefficientultralargemultiplesequencealignmentandphylogenetictreereconstructionwithdistributedandparallelcomputing |