Update README & Add CITATION

CITATION.cff

@@ -0,0 +1,8 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it as below.
+authors:
+- family-names: Shimoyama
+  given-names: Yuki
+title: "FastDTLmapper: Fast genome-wide DTL(Duplication-Transfer-Loss) event mapping tool"
+date-released: 2021-10-21
+url: "https://github.com/moshi4/FastDTLmapper"

README.md

@@ -51,7 +51,7 @@ Install latest development version with pip:
 
 ### Dependencies
 
-Python package dependencies list here (Auto installed with pip).
+Python package dependencies list here (auto installed with pip).
 
 Well known python package `numpy`, `pandas`, `scipy` and
 
@@ -62,35 +62,93 @@ Well known python package `numpy`, `pandas`, `scipy` and
 - [ETE3](http://etetoolkit.org/)  
   Tree analysis and visualization tool
 
-Following dependencies are packaged in **[src/fastdtlmapper/bin](https://github.com/moshi4/FastDTLmapper/tree/main/src/fastdtlmapper/bin)** directory.  
+Following dependencies are packaged in [src/fastdtlmapper/bin](https://github.com/moshi4/FastDTLmapper/tree/main/src/fastdtlmapper/bin) directory.  
 
-- [OrthoFinder](https://github.com/davidemms/OrthoFinder)  
+- [OrthoFinder](https://github.com/davidemms/OrthoFinder) [v2.5.2]  
   Orthology inference tool
-- [mafft](https://mafft.cbrc.jp/alignment/software/)  
+- [mafft](https://mafft.cbrc.jp/alignment/software/) [v7.487]  
   Sequences alignment tool
-- [trimal](http://trimal.cgenomics.org/)  
+- [trimal](http://trimal.cgenomics.org/) [v1.4]  
   Alignment sequences trim tool
-- [IQ-TREE](http://www.iqtree.org/)  
+- [IQ-TREE](http://www.iqtree.org/) [v2.1.3]  
   Phylogenetic tree reconstruction tool
+- [Treerecs](https://project.inria.fr/treerecs/) [v1.2]  
+  Multifurcated gene tree correction tool  
 - [AnGST](https://github.com/almlab/angst)  
   DTL reconciliation tool (Requires Python 2.X to run)
-- [parallel](https://www.gnu.org/software/parallel/)  
+- [parallel](https://www.gnu.org/software/parallel/) [v20200922]  
   Job parallelization tool (Requires Perl to run)
 
+<details>
+<summary>Dependencies Citation List</summary>
+
+BioPython:
+>Cock, P.J.A. et al.  
+>Biopython: freely available Python tools for computational molecular biology and bioinformatics. (2009)  
+>Bioinformatics 25(11) 1422-3  
+
+GOAtools:
+>Klopfenstein DV, Zhang L, Pedersen BS, ... Tang H  
+>GOATOOLS: A Python library for Gene Ontologyy analyses (2018)  
+>Scientific reports 8:10872  
+
+ETE:
+>Huerta-Cepas J., Serra F. and Bork P.  
+>ETE 3: Reconstruction, analysis and visualization of phylogenomic data (2016)  
+>Mol Biol Evol 33(6) 1635-1638
+
+OrthoFinder:
+>Emms D.M. & Kelly S.  
+>OrthoFinder: phylogenetic orthology inference for comparative genomics (2019)  
+>Genome Biology 20:238  
+
+MAFFT:
+>Yamada, Tomii, Katoh.  
+>Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees. (2016)  
+>Bioinformatics 32:3246-3251  
+
+trimAl:
+>Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon.  
+>trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. (2009)  
+>Bioinformatics 25: 1972-1973.  
+
+IQ-TREE:
+>B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear.  
+>IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. (2020)  
+>Mol. Biol. Evol. 37:1530-1534.  
+
+Treerecs:
+>Comte N, Morel B, Hasic D, Guéguen L, Boussau B, Daubin V, Penel S, Scornavacca C, Gouy M, Stamatakis A, et al.  
+>Treerecs: an integrated phylogenetic tool, from sequences to reconciliations (2020)  
+>Bioinformatics 36:4822–4824  
+  
+AnGST:
+>Lawrence A David and Eric J Alm.  
+>Rapid evolutionary innovation during an Archaean genetic expansion. (2010)  
+>Nature. 469(7328):93-6  
+
+parallel:
+>O. Tange  
+>GNU Parallel - The Command-Line Power Tool, ;login: (2011)  
+>The USENIX Magazine, February 2011:42-47.  
+  
+</details>
+
 ## Analysis Pipeline
 
+This is brief description of analysis pipeline. See [wiki](#overview) for details.
+
 1. Grouping ortholog sequences using OrthoFinder
 2. Align each OG(Ortholog Group) sequences using mafft
 3. Trim each OG alignment using trimal
 4. Reconstruct each OG gene tree using IQ-TREE
-5. DTL reconciliation of species tree & each OG gene tree using AnGST
-6. Aggregate and map genome-wide DTL reconciliation result
-
-This is summary description. See [wiki](#overview) for details.
+5. Correct each OG gene tree multifurcation using Treerecs
+6. DTL reconciliation of species tree & each OG gene tree using AnGST
+7. Aggregate and map genome-wide DTL reconciliation result
 
 ## Command Usage
 
-### Basic Run Command
+### Basic Command
 
     FastDTLmapper -i [fasta|genbank directory] -t [species tree file] -o [output directory]
 
@@ -118,10 +176,11 @@ If user set this option, input species tree must be ultrametric tree.
 
 #### Input Limitation
 
-- fasta or genbank files (--indir option)  
-  :warning: Following characters cannot be included in file name '_', '-', '|', '.'
-- species tree file (--tree option)  
-  :warning: Species name in species tree must match fasta or genbank file name
+fasta or genbank files (--indir option)  
+>:warning: Following characters cannot be included in file name '_', '-', '|', '.'  
+
+species tree file (--tree option)  
+>:warning: Species name in species tree must match fasta or genbank file name  
 
 ### Example Command
 
@@ -155,8 +214,9 @@ If user set this option, input species tree must be ultrametric tree.
     │   │   ├── OG0000000_aln_trim.fa        -- Trimmed OG alignement fasta file
     │   │   ├── OG0000000_dtl_map.nwk        -- OG DTL event mapped tree file
     │   │   ├── OG0000000_gain_loss_map.nwk  -- OG Gain-Loss event mapped tree file
-    │   │   ├── angst/                       -- AnGST DTL reconciliation result
-    │   │   └── iqtree/                      -- IQ-TREE gene tree reconstruction result
+    │   │   ├── iqtree/                      -- IQ-TREE gene tree reconstruction result
+    │   │   ├── treerecs/                    -- Treerecs multifurcated gene tree correction result
+    │   │   └── angst/                       -- AnGST DTL reconciliation result
     │   │
     │   ├── OG0000001/
     │   . 
@@ -180,7 +240,7 @@ If user set this option, input species tree must be ultrametric tree.
 
 FastDTLmapper subtool `plot_gain_loss_map` supports for plotting
 publication-ready gain/loss map figure as shown below.
-Users can plot easily and can output in any format they want by
+User can plot easily and can output in any format user want by
 changing plotting parameter.
 See [wiki](#overview) for details.