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### Identification of HGTs in eukaryotic genomes ###
###         Example: cow genome (bosTau7)        ###
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### System requirements:
    (1) Linux operation system, memory 4GB or up
    (2) Perl 5.8.5 or up
    (3) Software needed: lastz (1.04.00), RepeatMasker (4.0.7), BLAST (2.5.0+), cd-hit-est (4.6), muscle (3.8.31), FastTreeMP (2.1.9), etc.
    (4) Codes required:
    	A. analysis pipeline: pipeline.sh
	B. source code: all files in src/ (.perl)

### Installation guide:
    Obtain the analysis pipeline (pipeline.sh) and all files in src/

### Demo: Identify HGTs in cow genome, the above pipeline is an example
    (1) Datasets needed:
        A. genomes/: eukaryotic genomes
    	B. data/: RepeatMasker annotation, species id, etc.
    	C. fa/bosTau7.fa: cow reference genome
    (2) Intermediate results:
    	A. segment/: short fragments
	B. axt/: raw output of lastz alignment
	C. cov/, iden50/, iden70/, close/, remote/: screened alignment regions
	D. gradient/: gradient strategy to merge overlapped region with different CRG scale
	E. tree/: hit species for each candidate HGT
	F. ERV/: remove HGTs overlapped ERVs
    (3) final results:
    	A. noERV.fa: 100 non-redundant HGTs in cow genome
	B. tree-filtered/: phylogenetic trees of these HGTs

### Instructions for use:
    Prepare required datasets and code files, and keep them in right directories like that in demo.
    Then, follow the pipeline step by step

### Tips:
    Only pipeline, source code and final result are displayed here.
    To get more detailed datasets and intermediate results, please visit this site: http://cgm.sjtu.edu.cn/hgt (passwd:"2019hgtpasswd")