PlantTribes is a collection of automated modular analysis pipelines that utilize objective classifications of complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It post-processes de novo assembly transcripts into putative coding sequences and their corresponding amino acid translations, locally assembles targeted gene families, estimates paralogous/orthologous pairwise synonymous/non-synonymous substitution rates for a set of gene sequences, classifies gene sequences into pre-computed orthologous plant gene family clusters, and builds gene family multiple sequence alignments and their corresponding phylogenies. A user provides de novo assembly transcripts, and PlantTribes produces predicted coding sequences and their corresponding translations, a table of pairwise synonymous/non-synonymous substitution rates for reciprocal best blast transcript pairs, results of significant duplication components in the distribution of Ks (synonymous substitutions) values, a summary table for transcripts classified into orthologous plant gene family clusters with their corresponding functional annotations, gene family amino acid and nucleotide fasta sequences, multiple sequence alignments, and inferred maximum likelihood phylogenies. Optionally, a user can provide externally predicted coding sequences and their corresponding amino acid translations derived from a transcriptome assembly or gene predictions from a sequenced genome.
Please submit all questions, inquires, and bugs using the PlantTribes repository issues tab.
PlantTribes pipeline scripts have many external dependencies that need to be installed and available on the environment's $PATH before the pipelines can be used.
- AssemblyPostProcessor pipeline:
ESTScan (version 2.1), TransDecoder (version 3.0.1), HMMSearch (HMMER version 3.1b1),
MAFFT (version 7.215 ), trimAl (version 1.4.rev8), and GenomeTools (version 1.5.4). - GeneFamilyClassifier pipeline:
BLASTP (NCBI BLAST version 2.2.29+), and HMMScan (HMMER version 3.1b1). - PhylogenomicsAnalysis pipeline (legacy pipeline):
MAFFT (version 7.215 ), PASTA, trimAl (version 1.4.rev8), RAxML (version 8.1.16),
and FastTreeMP (version 2.1.7 SSE3). - GeneFamilyIntegrator:
No external dependencies required. - GeneFamilyAligner pipeline:
MAFFT (version 7.215 ), PASTA, and trimAl (version 1.4.rev8). - GeneFamilyPhylogenyBuilder pipeline:
RAxML (version 8.1.16), and FastTreeMP (version 2.1.7 SSE3). - KaKsAnalysis pipeline:
MAKEBLASTDB/BLASTN (NCBI BLAST version 2.2.29+), CRB-BLAST (version 0.6.9), MAFFT (version 7.215 ), PAML (version 4.8),
and EMMIX (version 1.3).
PlantTribes gene family scaffolds download website
- Open a terminal and change to the location where you would to keep PlantTribes.
- Example:
cd ~/softwares
- Clone the PlantTribes GitHub repository or download the zip archive and decompress it in your desired location.
- Examples:
git clone https://github.com/dePamphilis/PlantTribes.gitorunzip https://github.com/dePamphilis/PlantTribes/archive/master.zip
- Download the scaffold data set(s) that you would like to use into the PlantTribes' data subdirectory and decompress them.
- Examples:
cd PlantTribes/data,md5sum 22Gv1.1.tar.bz(should match the provided MD5 checksum for the data archive), followed bytar -xjvf 22Gv1.1.tar.bz2
The execulables for the PlantTribes pipelines are in the pipelines subdrectory of the installation. You can either add them to your PATH environment variable or execute directly from the PlantTribes installation.
- AssemblyPostProcessor pipeline:
- Display all usage options:
PlantTribes/pipelines/AssemblyPostProcessor
- Basic run using ESTScan prediction method:
PlantTribes/pipelines/AssemblyPostProcessor --transcripts transcripts.fasta --prediction_method estscan --score_matrices /path/to/score/matrices/Arabidopsis_thaliana.smat
- Display all usage options:
- GeneFamilyClassifier pipeline:
- Display all usage options:
PlantTribes/pipelines/GeneFamilyClassifier
- Basic run using 22Gv1.1 scaffolds, orthomcl clustering method, and blastp classifier:
PlantTribes/pipelines/GeneFamilyClassifier --proteins proteins.fasta --scaffold 22Gv1.1 --method orthomcl --classifier blastp
- Display all usage options:
- PhylogenomicsAnalysis pipeline (legacy pipeline):
- Display all usage options:
PlantTribes/legacy/PhylogenomicsAnalysis
- Basic run using 22Gv1.1 scaffolds, orthomcl clustering method, and raxml Phylogenetic trees inference method:
PlantTribes/pipelines/PhylogenomicsAnalysis --orthogroup_faa geneFamilyClassification_dir/orthogroups_fasta --scaffold 22Gv1.1 --method orthomcl --add_alignments --tree_inference raxml
- Display all usage options:
- GeneFamilyIntegrator:
- Display all usage options:
PlantTribes/pipelines/GeneFamilyIntegrator
- Basic run using 22Gv1.1 scaffolds, orthomcl clustering method:
GeneFamilyIntegrator --orthogroup_faa geneFamilyClassification_dir/orthogroups_fasta --scaffold 22Gv1.1 --method orthomcl
- Display all usage options:
- GeneFamilyAligner pipeline:
- Display all usage options:
PlantTribes/pipelines/GeneFamilyAligner
- Basic run using 22Gv1.1 scaffolds, orthomcl clustering method, and mafft alignment method:
GeneFamilyAligner --orthogroup_faa integratedGeneFamilies_dir --alignment_method mafft
- Display all usage options:
- GeneFamilyPhylogenyBuilder pipeline:
- Display all usage options:
PlantTribes/pipelines/GeneFamilyPhylogenyBuilder
- Basic run using 22Gv1.1 scaffolds, orthomcl clustering method, and fastree Phylogenetic trees inference method:
GeneFamilyPhylogenyBuilder --orthogroup_aln geneFamilyAlignments_dir/orthogroups_aln --tree_inference fasttree
- Display all usage options:
- KaKsAnalysis pipeline
- Display all usage options:
PlantTribes/pipelines/KaKsAnalysis
- Basic run using for paralogous analysis:
KaKsAnalysis --coding_sequences_species_1 species1.fna --proteins_species_1 species1.faa --comparison paralogs --num_threads 4
- Display all usage options:
Required Options:
--transcripts <string> : de novo transcriptome assembly fasta file (transcripts.fasta)
--prediction_method <string> : The prediction method for coding regions
If ESTScan: estscan
If TransDecoder: transdecoder
--score_matrices <string> : Required if the coding regions prediction method is ESTScan
(i.e. Arabidopsis_thaliana.smat, Oryza_sativa.smat, Zea_mays.smat)
Target Gene Family Assembly:
--gene_family_search <string> : File with a list of orthogroup identifiers for target gene families to assemble
Orthogroup identifiers can be obtained from the scaffold function annotation table -
"Orthogroup ID" field of .summary file in the config directory of the installation.
- requires "--scaffold" and "--method"
--scaffold <string> : Orthogroups or gene families proteins scaffold. This can either be an absolute
path to the directory containing the scaffolds (e.g., /home/scaffolds/22Gv1.1)
or just the scaffold (e.g., 22Gv1.1). If the latter, ~home/data is prepended to
the scaffold to create the absolute path.
If Monocots clusters (version 1.0): 12Gv1.0
If Angiosperms clusters (version 1.0): 22Gv1.0
If Angiosperms clusters (version 1.1): 22Gv1.1
If Green plants clusters (version 1.0): 30Gv1.0
If Other non PlantTribes clusters: XGvY.Z, where "X" is the number species in the scaffold,
and "Y.Z" version number such as 12Gv1.0. Please look at one of the PlantTribes scaffold
data on how data files and directories are named, formated, and organized.
--method <string> : Protein clustering method - required by "--gene_family_search"
If GFam: gfam
If OrthoFinder: orthofinder
If OrthoMCL: orthomcl
If Other non PlantTribes method: methodname, where "methodname" a nonempty string of
word characters (alphanumeric or "_"). No embedded special charaters or white spaces.
--gap_trimming <float> : Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0]
Default: 0.1
--min_coverage <float> : Minimum sequence coverage in the orthogroup trimmed protein multiple sequence alignment
Selecting transcripts with coverage of at least the average of the backbone orthogroup gene
models is recommended. Details in targeted gene family assembly summary statistics output file.
Default: 0.0 - [0.0 to 1.0]
Others Options:
--strand_specific : If de novo transcriptome assembly was performed with strand-specific library
Default: not strand-specific
--dereplicate : Remove reapeated sequences in predicted coding regions
--min_length <int> : Minimum sequence length of predicted coding regions
--num_threads <int> : number of threads (CPUs) - only required for targeted gene family assembly
Default: 1
Required Options:
--proteins <string> : Amino acids (proteins) sequences fasta file (proteins.fasta)
--scaffold <string> : Orthogroups or gene families proteins scaffold. This can either be an absolute
path to the directory containing the scaffolds (e.g., /home/scaffolds/22Gv1.1)
or just the scaffold (e.g., 22Gv1.1). If the latter, ~home/data is prepended to
the scaffold to create the absolute path.
If Monocots clusters (version 1.0): 12Gv1.0
If Angiosperms clusters (version 1.0): 22Gv1.0
If Angiosperms clusters (version 1.1): 22Gv1.1
If Green plants clusters (version 1.0): 30Gv1.0
If Other non PlantTribes clusters: XGvY.Z, where "X" is the number species in the scaffold,
and "Y.Z" version number such as 12Gv1.0. Please look at one of the PlantTribes scaffold
data on how data files and directories are named, formated, and organized.
--method <string> : Protein clustering method
If GFam: gfam
If OrthoFinder: orthofinder
If OrthoMCL: orthomcl
If Other non PlantTribes method: methodname, where "methodname" a nonempty string of
word characters (alphanumeric or "_"). No embedded special charaters or white spaces.
--classifier <string> : Protein classification method
If BLASTP: blastp
If HMMScan: hmmscan
If BLASTP and HMMScan: both
Others Options:
--config_dir <string> : (Optional) Absolute path to the directory containing the default configuration files
for the selected scaffold defined by the value of the --scaffold parameter (e.g.,
/home/configs/22Gv1.1). If this parameter is not used, the directory containing the
default configuration files is set to ~home/config.
--num_threads <int> : number of threads (CPUs) to used for HMMScan, BLASTP, and MAFFT
Default: 1
--super_orthogroups <string> : SuperOrthogroups MCL clustering - blastp e-value matrix between all pairs of orthogroups
If minimum e-value: min_evalue (default)
If average e-value: avg_evalue
--single_copy_custom <string> : Configuration file for single copy orthogroup custom selection - incompatible with
"--single_copy_taxa". This must be an absolute path to the configuration file
(e.g., '~/home/scaffolds/22Gv1.1.singleCopy.config') or the string 'default'. If the
latter, the config is defined to be ~/config_dir/~scaffold.singleCopy.config. See the
single copy configuration files the config sub-directory of the installation on how to
customize the single copy selection.
--single_copy_taxa <int> : Minimum single copy taxa required in orthogroup - incompatible with "--single_copy_custom"
--taxa_present <int> : Minimum taxa required in single copy orthogroup - requires "--single_copy_taxa"
--orthogroup_fasta : Create orthogroup fasta files - requires "--coding_sequences" for CDS orthogroup fasta
--coding_sequences <string> : Corresponding coding sequences (CDS) fasta file (cds.fasta)
Required Options:
--orthogroup_faa <string> : Directory containing gene family classification orthogroups protein fasta files
--scaffold <string> : Orthogroups or gene families proteins scaffold. This can either be an absolute
path to the directory containing the scaffolds (e.g., /home/scaffolds/22Gv1.1)
or just the scaffold (e.g., 22Gv1.1). If the latter, ~home/data is prepended to
the scaffold to create the absolute path.
If Monocots clusters (version 1.0): 12Gv1.0
If Angiosperms clusters (version 1.0): 22Gv1.0
If Angiosperms clusters (version 1.1): 22Gv1.1
If Green plants clusters (version 1.0): 30Gv1.0
If Other non PlantTribes clusters: XGvY.Z, where "X" is the number species in the scaffold,
and "Y.Z" version number such as 12Gv1.0. Please look at one of the PlantTribes scaffold
data on how data files and directories are named, formated, and organized.
--method <string> : Protein clustering method
If GFam: gfam
If OrthoFinder: orthofinder
If OrthoMCL: orthomcl
If Other non PlantTribes method: methodname, where "methodname" a nonempty string of
word characters (alphanumeric or "_"). No embedded special charaters or white spaces.
Multiple Sequence Alignments:
--create_alignments : Create orthogroup protein multiple sequence alignments including scaffold backbone proteins
(MAFFT algorithm, incompatible with "--add_alignments" and "--pasta_alignments")
--add_alignments : Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments
(MAFFT algorithm, incompatible with "--create_alignments" and "--pasta_alignments")
--pasta_alignments : Create orthogroup protein multiple sequence alignments including scaffold backbone proteins
(PASTA algorithm, incompatible with "--create_alignments" and "--add_alignments")
--codon_alignments : Construct orthogroup multiple codon alignments - requires "--orthogroup_fna"
--iterative_realignment <int> : Iterative orthogroups realignment, trimming and fitering - requires "--remove_sequences"
(maximum number of iterations)
Phylogenetic Trees:
--tree_inference <string> : Phylogenetic trees inference method
If RAxML: raxml
If FastTree: fasttree
--max_orthogroup_size <int> : Maximum number of sequences in orthogroup alignments
Default: 100
--min_orthogroup_size <int> : Minimum number of sequences in orthogroup alignments
Default: 4
--sequence_type <string> : Sequence type used in the phylogenetic inference - "dna" requires "--codon_alignments"
If amino acid based: protein (default)
If nucleotide based: dna
--rooting_order <string> : File with a list of string fragments matching sequences identifiers of species in the
classification (including scaffold taxa) to be used for determining the most basal taxa in
the orthogroups for rooting trees. Should be listed in decreasing order from older to younger
lineages. If the file is not provided, trees will be rooted using the most distant taxon
present in the orthogroup (see example rooting order configuration files in config sub-directory
of the installation).
- requires "--tree_inference" with RAxML
--bootstrap_replicates <int> : Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree
- requires "--tree_inference" with RAxML
Default: 100
MSA Quality Control Options:
--automated_trimming : Trims alignments using trimAl's ML heuristic trimming approach - incompatible "--gap_trimming"
--gap_trimming <float> : Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0]
--remove_sequences <float> : Removes gappy sequences in alignments (i.e. 0.5 removes sequences with 50% gaps): [0.1 to 1.0]
- requires either "--automated_trimming" or "--gap_trimming"
Others Options:
--config_dir <string> : (Optional) Absolute path to the directory containing the default configuration files
for the selected scaffold defined by the value of the --scaffold parameter (e.g.,
/home/configs/22Gv1.1). If this parameter is not used, the directory containing the
default configuration files is set to ~home/config.
--num_threads <int> : number of threads (CPUs) to assign to external utilities (MAFFT, PASTA, and RAxML)
Default: 1
--max_memory <int> : maximum memory (in mb) available to PASTA's java tools - requires "--pasta_alignments"
Default: 256
--pasta_iter_limit <int> : Maximum number of iteration that the PASTA algorithm will run - requires "--pasta_alignments"
Default: 3
--orthogroup_fna : Corresponding gene family classification orthogroups CDS fasta files. Files should be in the
same directory with input orthogroups protein fasta files.
Required Options:
--orthogroup_fasta <string> : Directory containing gene family classification orthogroups fasta files
--scaffold <string> : Orthogroups or gene families proteins scaffold. This can either be an absolute
path to the directory containing the scaffolds (e.g., /home/scaffolds/22Gv1.1)
or just the scaffold (e.g., 22Gv1.1). If the latter, ~home/data is prepended to
If Monocots clusters (version 1.0): 12Gv1.0
If Angiosperms clusters (version 1.0): 22Gv1.0
If Angiosperms clusters (version 1.1): 22Gv1.1
If Green plants clusters (version 1.0): 30Gv1.0
If Other non PlantTribes clusters: XGvY.Z, where "X" is the number species in the scaffold,
and "Y.Z" version number such as 12Gv1.0. Please look at one of the PlantTribes scaffold
data on how data files and directories are named, formated, and organized.
--method <string> : Protein clustering method for the classification scaffold
If GFam: gfam
If OrthoFinder: orthofinder
If OrthoMCL: orthomcl
If Other non PlantTribes method: methodname, where "methodname" a nonempty string of
word characters (alphanumeric or "_"). No embedded special charaters or white spaces.
Required Options:
--orthogroup_faa <string> : Directory containing gene family classification orthogroup protein fasta files
--alignment_method <string> : Multiple sequence alignment method:
If MAFFT algorithm: mafft
If PASTA algorithm: pasta
Codon Alignments:
--codon_alignments : Construct orthogroup multiple codon alignments - corresponding gene family classification
orthogroups CDS fasta files should be in the same directory with input orthogroups protein
fasta files.
MSA Quality Control Options:
--automated_trimming : Trims alignments using trimAl's ML heuristic trimming approach - incompatible "--gap_trimming"
--gap_trimming <float> : Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0]
--remove_sequences <float> : Removes gappy sequences in alignments (i.e. 0.7 removes sequences with more than 30% gaps): [0.1 to 1.0]
- requires either "--automated_trimming" or "--gap_trimming"
--iterative_realignment <int> : Iterative orthogroups realignment, trimming and fitering - requires "--remove_sequences"
(maximum number of iterations)
Others Options:
--config_dir <string> : (Optional) Absolute path to the directory containing the default configuration files
for the selected scaffold defined by the value of the --scaffold parameter (e.g.,
--num_threads <int> : number of threads (CPUs) to assign to external utilities (MAFFT and PASTA)
Default: 1
--max_memory <int> : maximum memory (in mb) available to PASTA's java tools - requires "--alignment_method = pasta"
Default: 256
--pasta_iter_limit <int> : Maximum number of iteration that the PASTA algorithm will run - requires "--alignment_method = pasta"
Default: 3
--pasta_script_path <string> : Optional path to the location of the run_pasta.py script. which is used for running PASTA
from the command line (useful since the script is a .py file). Using this will override
the default defined in ~home/config/plantTribes.
Required Options:
--orthogroup_aln <string> : Directory containing gene family orthogroup alignment file
--tree_inference <string> : Phylogenetic trees inference method
If RAxML: raxml
If FastTree: fasttree
Others Options:
--scaffold <string> : Orthogroups or gene families proteins scaffold. This can either be an absolute
path to the directory containing the scaffolds (e.g., /home/scaffolds/22Gv1.1)
or just the scaffold (e.g., 22Gv1.1). If the latter, ~home/data is prepended to
the scaffold to create the absolute path.
If Monocots clusters (version 1.0): 12Gv1.0
If Angiosperms clusters (version 1.0): 22Gv1.0
If Angiosperms clusters (version 1.1): 22Gv1.1
If Green plants clusters (version 1.0): 30Gv1.0
If Other non PlantTribes clusters: XGvY.Z, where "X" is the number species in the scaffold,
and "Y.Z" version number such as 12Gv1.0. Please look at one of the PlantTribes scaffold
data on how data files and directories are named, formated, and organized.
--method <string> : Protein clustering method for the classification scaffold
If GFam: gfam
If OrthoFinder: orthofinder
If OrthoMCL: orthomcl
If Other non PlantTribes method: methodname, where "methodname" a nonempty string of
word characters (alphanumeric or "_"). No embedded special charaters or white spaces.
--config_dir <string> : (Optional) Absolute path to the directory containing the default configuration files
for the selected scaffold defined by the value of the --scaffold parameter (e.g.,
/home/configs/22Gv1.1). If this parameter is not used, the directory containing the
default configuration files is set to ~home/config.
--max_orthogroup_size <int> : Maximum number of sequences in orthogroup alignments
Default: 100
--min_orthogroup_size <int> : Minimum number of sequences in orthogroup alignments
Default: 4
--rooting_order <string> : File with a list of string fragments matching sequences identifiers of species in the
classification (including scaffold taxa) to be used for determining the most basal taxa in
the orthogroups for rooting trees. Should be listed in decreasing order from older to younger
lineages. If the file is not provided, trees will be rooted using the most distant taxon
present in the orthogroup (see example rooting order configuration files in config sub-directory
of the installation).
- requires "--tree_inference" with RAxML
--bootstrap_replicates <int> : Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree
- requires "--tree_inference" with RAxML
Default: 100
--num_threads <int> : number of threads (CPUs) to assign to external utilities (RAxML)
Default: 1
Required Options:
--coding_sequences_species_1 <string> : Coding sequences (CDS) fasta file for the first species (species1.fna)
--proteins_species_1 <string> : Amino acids (proteins) sequences fasta file for the first species (species1.faa)
--comparison <string> : pairwise sequence comparison to determine homolgous pairs
If self species comparison: paralogs
If cross species comparison: orthologs (requires second species data)
Others Options:
--coding_sequences_species_2 <string> : Coding sequences (CDS) fasta file for the first species (species2.fna)
requires "--comparison" to be set to "orthologs"
--proteins_species_2 <string> : Amino acids (proteins) sequences fasta file for the first species (species2.faa)
requires "--comparison" to be set to "orthologs"
--crb_blast <string> : Use conditional reciprocal best BLAST to determine for cross-species orthologs
instead of the default reciprocal best BLAST - requires "--comparison" to be set to "orthologs
--min_coverage <float> : Minimum sequence pairwise coverage length between homologous pairs
Default: 0.5 (50% coverage) - [0.3 to 1.0]
--recalibration_rate <float> : Recalibrate synonymous substitution (ks) rates of a species using a predetermined evolutionary
rate that can be determined from a species tree inferred from a collection single copy genes
from taxa of interest (Cui et al., 2006) - applies only paralogous ks
--codeml_ctl_file <string> : PAML's codeml control file to carry out ML analysis of protein-coding DNA sequences using codon
substitution models. The defaults in the "codeml.ctl.args" template in the config directory
of the installation will be used if not provided. NOTE: input (seqfile, treefile) and output
(outfile) parameters of codeml are not included in the template.
--fit_components : Fit a mixture model of multivariate normal components to synonymous (ks) distribution to
identify significant duplication event(s) in a genome
--num_of_components <int> : Number components to fit to synonymous substitutions (ks) distribution - required if
"--fit_components"
--min_ks <float> : Lower limit of synonymous substitutions (ks) - necessary if fitting components to the
distribution to reduce background noise from young paralogous pairs due to normal gene births
and deaths in a genome.
--max_ks <float> : Upper limit of synonymous substitutions (ks) - necessary if fitting components to the
distribution to exclude likey ancient paralogous pairs.
--num_threads <int> : number of threads (CPUs)
Default: 1
PlantTribes is distributed under the GNU GPL v3. For more information, see license.