iqtree2

IQ-TREE2

About: |

Thanks to the recent advent of next-generation sequencing techniques, the amount of phylogenomic/transcriptomic data have been rapidly accumulated. This extremely facilitates resolving many “deep phylogenetic” questions in the tree of life. At the same time it poses major computational challenges to analyze such big data, where most phylogenetic software cannot handle. Moreover, there is a need to develop more complex probabilistic models to adequately capture realistic aspects of genomic sequence evolution.

Documentation : http://www.iqtree.org/doc/

Citation : http://www.iqtree.org/doc/Home#how-to-cite-iq-tree

Directory tree:

iqtree2/
├── iqtree.ckp.gz
├── iqtree.contree
├── iqtree.iqtree
├── iqtree.log
├── iqtree.splits.nex
├── iqtree.treefile
└── iqtree.treefile.nwk

Example files:

consesnsus tree iqtree.contree

(GCF_000788095.1_ASM78809v1_genomic:0.0226855589,GCF_000758465.1_ASM75846v1_genomic:0.0242346496,(((GCF_000834105.1_ASM83410v1_genomic:0.1216464232,GCF_000972335.1_ASM97233v1_genomic:0.1326421611)100:0.0758826018,GCF_000978875.1_ASM97887v1_genomic:0.0288472196)100:0.0077171799,GCF_000742995.1_ASM74299v1_genomic:0.0272140769)100:0.0095841393);

with bootstraps iqtree.treefile

(GCF_000788095.1_ASM78809v1_genomic:0.0226859990,GCF_000758465.1_ASM75846v1_genomic:0.0242347825,(((GCF_000834105.1_ASM83410v1_genomic:0.1216485754,GCF_000972335.1_ASM97233v1_genomic:0.1326448390)100/100:0.0758847478,GCF_000978875.1_ASM97887v1_genomic:0.0288508717)100/100:0.0077156748,GCF_000742995.1_ASM74299v1_genomic:0.0272142934)100/100:0.0095840148);

compatible with microcreate (same as iqtree.treefile, but has the .nwk at the end) iqtree.treefile.nwk

(GCF_000788095.1_ASM78809v1_genomic:0.0226859990,GCF_000758465.1_ASM75846v1_genomic:0.0242347825,(((GCF_000834105.1_ASM83410v1_genomic:0.1216485754,GCF_000972335.1_ASM97233v1_genomic:0.1326448390)100/100:0.0758847478,GCF_000978875.1_ASM97887v1_genomic:0.0288508717)100/100:0.0077156748,GCF_000742995.1_ASM74299v1_genomic:0.0272142934)100/100:0.0095840148);