{"id":20386972,"url":"https://github.com/cmdcolin/tenest","last_synced_at":"2025-09-24T00:31:33.117Z","repository":{"id":218956551,"uuid":"747783181","full_name":"cmdcolin/TEnest","owner":"cmdcolin","description":"A backup of the source code for TEnest, found on archive.org","archived":false,"fork":false,"pushed_at":"2024-01-24T20:03:28.000Z","size":8694,"stargazers_count":3,"open_issues_count":0,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-06T04:23:36.307Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cmdcolin.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-01-24T16:24:27.000Z","updated_at":"2024-10-10T18:55:12.000Z","dependencies_parsed_at":"2024-11-15T02:42:01.173Z","dependency_job_id":"dbfbc1ad-8076-4b53-a6c4-5c1e6bbdc95b","html_url":"https://github.com/cmdcolin/TEnest","commit_stats":null,"previous_names":["cmdcolin/tenest"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/cmdcolin/TEnest","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2FTEnest","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2FTEnest/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2FTEnest/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2FTEnest/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cmdcolin","download_url":"https://codeload.github.com/cmdcolin/TEnest/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2FTEnest/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":276673732,"owners_count":25683939,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-23T02:00:09.130Z","response_time":73,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-15T02:41:55.502Z","updated_at":"2025-09-24T00:31:30.468Z","avatar_url":"https://github.com/cmdcolin.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Intro\n\nTEnest is a tool for finding and annotating transposable element (TE) insertions\n\nThis source code is marked as the v2 version (v2 pub here\nhttps://pubmed.ncbi.nlm.nih.gov/23918438/, v1 pub here\nhttps://pubmed.ncbi.nlm.nih.gov/18032588/)\n\n![](img/1.png)\n\nExample of TEnest output\n\n## Organism Repeat Databases:\n\nArchive links from 2015\n\n- [WHEAT](./WHEAT) (from archive.org\n  [WHEAT.tar.gz](https://web.archive.org/web/20150806130046/http://www.public.iastate.edu/~imagefpc/Subpages/TE_nest/WHEAT.tar.gz))\n- [RICE](./RICE) (from archive.org\n  [RICE.tar.gz](https://web.archive.org/web/20150806130046/http://www.public.iastate.edu/~imagefpc/Subpages/TE_nest/RICE.tar.gz))\n- [BARLEY](./BARLEY) (from archive.org\n  [BARLEY.tar.gz](https://web.archive.org/web/20150806130046/http://www.public.iastate.edu/~imagefpc/Subpages/TE_nest/BARLEY.tar.gz))\n- [MAIZE](./MAIZE) (from archive.org\n  [source](https://web.archive.org/web/20150806130046/http://www.public.iastate.edu/~imagefpc/Subpages/TE_nest/MAIZE.tar.gz))\n\n## TEnest v2 README.txt\n\nSee also the v1 README.txt, it has a bit different content\nhttps://github.com/cmdcolin/TEnest/tree/v1.0.0 adapted from the webpage at this\narchive link in the 2010 copy of the page\nhttps://web.archive.org/web/20100508181248/http://www.public.iastate.edu/~imagefpc/Subpages/te_nest.html\n\nThis v2 README is adapted from this 2015 copy of the same page\nhttps://web.archive.org/web/20150806130028/http://www.public.iastate.edu/~imagefpc/Subpages/TE%20nest%202.0%20Readme.txt\n\n### Overview\n\nTEnest annotates TE insertions in a given input sequence. A repeat database is\nused to identify TEs and to provide the reference for reconstructing degraded\nTEs to their ancestral state. The nesting structure of TEs is determined by\nanalysis of TE insertion locations; age since insertion of LTR retrotransposons\nis calculated from LTR divergence. A graphical display of the annotated TEs is\nprovided to visualize the chronological nesting structure. Both a web version\nand a downloadable linux command line version of TEnest are available; in the\nfollowing descriptions the command line version is discussed. Many, but not all\nof the explained options are also available on the web version of TEnest.\n\n### Transposable Element Sequence Databases\n\nTEnest utilizes organism specific TE databases to annotate repeats by sequence\nalignment. Several pre-constructed TE databases are supplied with TEnest and\nalso available on the online PlantGDB [13] version of TEnest. Pre-constructed TE\ndatabases include maize, rice, wheat and Hordeum vulgare (barley). A TEnest\ndatabase consists of two files per organism; full-length sequences for all TEs\nin multi-FASTA format [14], and a four column table with an entry for each TE in\nthe multi-FASTA file. The TEnest database sequence and table files are named\nfirst by organism and appended with `_TEnest.fasta` and `_TEnest.table`,\nrespectively. Users can switch between organism TE databases using the option\n`--org organism`.\n\nThe TEnest database table has four tab-delimited columns. The first is the TE\nname, and corresponds to the header of the full-length TE sequence with the\nright chevron removed and trimmed at the first white space. Therefore, '\u003eopie\nretrotransposon' becomes 'opie'. The second column is the classification of this\nTE. This is a one-word designator from a controlled list, and as such, only the\nfollowing classification terms can be used: LTR_retrotransposon,\nNon-LTR_retrotransposon, DNA_transposon. However this controlled list can be\nchanged by using the options `--te_controlled_list_ltr` for LTR\nretrotransposons, `--te_controlled_list_other` for non-LTR retrotransposons and\nDNA transposons, and entering the lists of the altered classification names for\neach of the options in double quotes. The last two columns are reserved only for\nLTR retrotransposons. An LTR is defined here by the start and stop coordinates\nfrom the full-length TE. Either the right- or left-most LTR coordinate positions\ncan be used.\n\nConstruction of a custom TE database is also possible. Users can add to one of\nthe existing pre-constructed databases, remove TEs from one of the available\ndatabases, or construct a fully novel TE database. To add TEs to an existing\ndatabase, copy the original database files to newly named file,\n`maize_TEnest.fasta` becomes `maize_custom_TEnest.fasta`, and likewise for the\ntable file. New full-length TE sequences can be appended to the new fasta file\nand new entries are added to the table file. If the new entry is an LTR\nretrotransposon, be sure to enter coordinates for the LTR location. Finally\npoint TEnest to the new sequence database by using the option --org\nmaize_custom. The process is much easier to remove a TE from the sequence\ndatabase. Simply changing the classification field in the sequence database\ntable to a non-approved value will cause TEnest to ignore the TE from analysis.\nTo construct a new TEnest sequence database, follow the above descriptions to\ncreate both the full-length multi-FASTA TE sequence file and the associated\ntable, making sure the TE classifications agree with the controlled TE list.\n\n### Installing TEnest\n\nTEnest comes packaged with the TEnest.pl perl program, the graphical display\nprogram of TEnest, svg_ltr.pl, the TEnest sequence databases, and a\nlong-sequence submission script split_TEnest.pl explained in the special\nanalysis section (2.4.6 below). TEnest utilizes two third-party software\nprograms that must be obtained from their respective sources; NCBI BLAST [12]\nfor the quick identification of potential TE alignment regions, and LALIGN [15]\n(available at http://faculty.virginia.edu/wrpearson/fasta/fasta2/) from the\nFASTA2 software suite [16] for local alignments of TEs to the reference\nsequence.\n\nOnce BLAST and LALIGN are installed, download the zipped TEnest.tar.gz file and\nthe TE database files. Move them to the installation directory and unzip with\nthe command `tar --xzf \\*.tar.gz`. Several parameters in the TEnest program must\nbe updated to integrate each of the BLAST and LALIGN program capabilities. Open\nthe TEnest.pl file for editing and change each of the following location\nvariables to point to the correct files or directories:\n\n#### Database location:\n\nPoint this to the directory where your TEnest database files are found. For\nexample, if the maize_TEnest.fasta and maize_TEnest.table are found.\n\n`$db_directory = '/home/user/TEnest/DB';`\n\n#### Output location:\n\nThe default location for TEnest output is your current working directory.\nHowever you can alter this to always write to the same location.\n\n`$output_directory = '/home/user/TEnest';`\n\n#### NCBI-BLAST Executables:\n\nThe path needed to run BLAST. If blastall is in your path this can be left\nblank.\n\n`$blast_directory = '/usr/local/bin';`\n\n#### FASTA LALIGN Executable:\n\nThe path needed to run LALIGN. If LALIGN is in your path this can be left blank.\n\n`$lal_directory = '/usr/local/bin/FASTA2';`\n\nOnce complete, save and close the TEnest.pl program. Make the file executable\nwith the command `chmod +x TEnest.pl`. Add the TEnest directory to your\nexecutable path.\n\n### Running TEnest\n\nThe general command for a TEnest analysis is\n`TEnest.pl my_input.fasta [options]`.\n\nMany options are available for fine tuning and customizing TEnest runs. Each of\nthese options can be entered via the command line; they are explained below by\nsection corresponding to the different processes of TEnest.\n\n#### LTR Identification\n\nIn the first stage of TEnest, LTR sequences are extracted from the TE database\nand aligned to the input sequence. A two-phase alignment process designed to\nprovide quick but accurate alignments over long sequence regions is accomplished\nusing BLAST coupled with a pairwise alignment. Nucleotide BLAST gives a TEnest a\nvery general overview of where TEs may reside on the input sequence. Due to\ntheir sequence similarity multiple TEs may be identified at the same location on\nthe input sequence by the BLAST alignment. Each of the regions identified by\nBLAST are then put into a pairwise local alignment process using LALIGN. Here a\ndecision is made to identify the best-matching TE also finding the exact start\nand stop positions of the match.\n\nOnce alignments are complete, a set of fragmented LTR annotations have been\ncreated. Progressing through each TE, the fragments are joined to recreate full\nLTR sequences. There are multiple reasons LTRs might be fragmented: there may\ndifferences between the input sequence version and the database version; nested\ninsertions of TEs may have caused a sequence split and distance separation\nwithin the LTR; or sequence gaps or mis-assemblies have created an artificial\nsplit. In any case, recombination attempts to identify LTR fragments and create\nfull-length groups. All sequential LTR fragment combinations are created and\ntheir LTR-based coordinates are considered for re-combination possibilities.\n\nOnce full-length LTR sequences have been recombined, TEnest enters the LTR\npairing phase where the left and right LTRs of a retrotransposon are identified.\nDue to the insertion process of LTR retrotransposons, the left and right LTR are\nsequence twins at the time of insertion. Over evolutionary time the two LTRs\nwill accumulate mutations independently [17]. TEnest uses these mutations to\nidentify a paired set of LTRs. The left and right LTRs of a retrotransposon will\nhave more similar sequence to each other than to other LTRs of the same TE type.\nThe base substitution rate (BSR) between all LTRs is calculated via LTR\nalignments, the LTR with most similar sequences are paired together. BSR is\ndetermined by the amount of single mutations between the two LTRs divided by the\nLTR alignment length. A maximum distance between left and right LTRs can be used\nto prevent unlikely long range TE insertions. Also, a filtering process for LTR\npairing can be used to speed up the process and prevent incorrect combinations.\nWhen the option `--ltr_find_LR` is used, TEnest will attempt to designate each\nLTR as either a left or right copy prior to the pairing process by identifying a\nsequence junction between the LTR and internal region. Not all LTRs will be able\nto be classified as left or right if the junction sequence is not present. Left,\nright and unknown designated LTRs are then sent to the LTR pairing process where\nleft-left, right-right and right-left (accounting for reverse-complementation)\ncombinations are excluded. Finally, age since insertion in Mya is calculated,\nthe BSR is divided by two times the substitution rate in repetitive regions in\ngrasses (1.3 x 10-8) [6, 7]. LTRs that are not identified as paired will be\nclassified as solo-LTRs.\n\n### Alignment Options\n\n- `--ltr_blast_cutoff` Expectation value of the LTR BLASTN [1e-01]\n\n- `--ltr_gap_open` LTR alignment gap open (LALIGN --f parameter) [30]\n\n- `--ltr_gap_ext` LTR alignment gap extension (LALIGN --g parameter) [15]\n\n- `--ltr_gap_rep` LTR alignments to report within sub-region (LALIGN --k\n  parameter) [7]\n\n- `--ltr_lal_score` Parsed expectation value of the LTR local alignment, where\n  20 equals 1e-20 [20]\n\n### LTR Reconstruction Options\n\n- `--ltr_smallest` Shortest length in bp of LTR fragment allowed to attempt LTR\n  reconstruction. Very small fragments may be non-TE hits and will exponentially\n  inflate the powerset function. [25]\n\n- `--ltr_overlap` Length in bp of LTR-based coordinates to allow when combining\n  LTR fragments in the LTR alignment phase. A size of 0 will allow no overlap.\n  [25]\n\n- `--ltr_full_shortest` Shortest length in bp of LTRs after reconstruction. Any\n  LTRs less than this value will be ignored. [50]\n\n- `--ltr_pwr_max` Longest length in bp that the gap between LTR fragments can\n  span. If the length between two fragments is greater the sections cannot be\n  joined. [100000]\n\n- `--ltr_bad_set` LTRs are reconstructed using their LTR-based coordinates to\n  identify the entire LTR sequence. Two regions with alike positions cannot\n  belong to the same LTR insertion and therefore do not need to attempt\n  reconstruction. This parameter allows wobble between calling two LTR fragments\n  alike, for example a value of 5 will identify LTRs with coordinates 100-200\n  and 102-197 as the same position. [5]\n\n### LTR Pairing Options\n\n- `--ltr_find_LR` Invoke the process to identify left and right LTRs prior to\n  LTR pairing. T/F [T]\n\n- `--ltr_bsr_length` Greatest distance in bp to allow between paired left and\n  right LTRs. A value of 0 will not invoke distance restriction. [250000]\n\n- `--bsr_gap_open` Paired LTR alignment gap open (LALIGN --f parameter) [12]\n\n- `--bsr_gap_ext` Paired LTR alignment gap extension (LALIGN --g parameter) [4]\n\n- `--bsr_max` Max BSR value to allow between LTR pairs [0.6]\n\n## Identification of Internal Regions of LTR Retrotransposons\n\nTEnest attempts to identify the internal regions for LTRs paired in the previous\nprocesses. Starting with the smallest distanced set first, TEnest cycles through\nall paired LTRs and aligns the internal sequence to the expected TE. Matching\nsequence again goes through the recombination process described above to create\nfull-length joined internal regions. The annotated LTRs and internal region\nsequences are masked (changed to 'N' but retaining the sequence length), and the\nnext longest spanning LTR set is analyzed. Masking the sequence prior to the\nnext alignment run prevents a nested TE from matching to multiple LTR pairs,\nespecially a problem when the same TE types are nested within one another.\n\n### Local Alignment Options\n\n- `--mid_gap_open` MID alignment gap open (LALIGN --f parameter) [75]\n\n- `--mid_gap_ext` MID alignment gap extension (LALIGN --g parameter) [75]\n\n- `--mid_gap_rep` MID alignments to report within sub-region (LALIGN --k\n  parameter) [5]\n\n- `--mid_lal_score` Parsed expectation value of the MID local alignment, where\n  20 equals 1e-20 [20]\n\n### Internal Region Reconstruction Options\n\n- `--mid_smallest` Shortest length in bp of fragment allowed to enter\n  reconstruction. Very small fragments may be non-TE hits and will exponentially\n  inflate the powerset function. [25]\n\n- `--mid_overlap` Length in bp of TE-based coordinates to allow when combining\n  MID fragments in the alignment phase. A size of 0 will allow no overlap. [25]\n\n- `--mid_bad_set` Basepair wobble range to consider MID fragments as identical\n  and prevent both segments from entering powerset reconstruction. (see\n  --ltr_bad_set for more information) [5]\n\n## Fragmented Retrotransposons and non-LTR Transposable Elements\n\nAll un-annotated regions make one final pass through TE identification. In this\nround the goal is to identify both fragmented LTR retrotransposons that did not\nhave a paired set of LTRs identified and non-LTR containing TEs. The full set of\nTEs from the sequence database; LTR retrotransposons and other Class I\nretrotransposons such as LINEs and SINEs, along with all Class II TEs go through\nthe previously described two phase alignment process. Again, split annotated TE\nregions are joined through the recombination process also previously described.\nAfter reconstruction, TEs are classified as fragmented. Their full annotation\nlength is compared to their expected full TE length, if 80% of the TE was\nidentified the annotation is promoted to a non-LTR full-length classification.\n\nFinally, a round of conflict checks takes place. All combinations of joined or\npaired TE sections are checked against all other joined groups to identify any\ndisagreeing recombined sets. TEnest requires all TE insertions to be annotated\nin such a way as to show the chronological order of TE nesting. TEnest will not\ngroup TE sections if a later recombination has rearranged the sequence order. If\na TE has nested within an older TE insertion, the full annotated sequence of the\nnewer TE must be found within the older TE. If sequence order conflicts are\nseen, the TE with less sequence identity to the TE database entry is split into\nnon-conflicting fragmented sections.\n\n## Local Alignment Options\n\n- `--fn_gap_open` Fragment alignment gap open (LALIGN --f parameter) [75]\n\n- `--fn_gap_ext` Fragment alignment gap extension (LALIGN --g parameter) [75]\n\n- `--fn_gap_rep` Fragment alignments to report within sub-region (LALIGN --k\n  parameter) [5]\n\n- `--fn_lal_score` Parsed expectation value of the local alignment, where 20\n  equals 1e-20 [20]\n\n## Internal Region Reconstruction Options\n\n- `--fn_smallest` Shortest length in bp of fragment allowed to enter\n  reconstruction. Very small fragments may be non-TE hits and will exponentially\n  inflate the powerset function. [25]\n\n- `--fn_overlap` Length in bp of TE-based coordinates to allow when combining\n  fragments in the alignment phase. A size of 0 will allow no overlap. [25]\n\n- `--fn_bad_set` Basepair wobble range to consider fragments as identical and\n  prevent both segments from entering powerset reconstruction. (see\n  --ltr_bad_set for more information). [5]\n\n### TEnest Output Files\n\nUpon completion TEnest.pl provides three files. The first is a repeat-masked\nFASTA format sequence file similar to the output of RepeatMasker [18]. The\nsecond is a generic feature format version 3 (GFF3) output of the nested TE\nannotations for use in genome viewers such as GBrowse [19]. The third is a\ncoordinate file of the annotated TEs identified in the input sequence. This file\nis named with 'LTR' as the file extension, and is used as the input for the\nTEnest graphical display program. Four sections in the LTR output file\ncorrespond to the following annotation classifications: 1) solo-LTRs identified\nas LTRs without pairs (SOLO), 2) full LTR retrotransposon composed of paired\nLTRs and internal regions (PAIR), 3) fragmented LTR retrotransposons (FRAG),\nand 4) full length non-LTR TEs (NLTR). The SOLO, FRAG and NLTR entries each have\na header line that contains the classification, a unique TE identifier, the TE\nname, and the direction of the TE relative to the TE database reference\nsequence. The following line contains the coordinates of the TE annotation,\nfirst the start and stop positions in the input sequence, secondly the start and\nstop positions in the reference TE sequence. The PAIR entries are similar to the\nother sections with two differences. The PAIR header line has a BSR value\nfollowing the direction entry, and there are three coordinate lines\ncorresponding to the left (L), right (R), and internal regions (M). Output files\nwill be written to an output directory named in the format\n`TEnest_date-time_my_input.fasta`.\n\n### TEnest Graphical Display\n\nDue to the nested structure of TE insertions, even with TEnest annotations the\narrangement of the repetitive sequence can be difficult to understand.\nTherefore, TEnest provides an auxiliary graphical display program to visualize\nthe coordinate annotation file. As shown in, svg_ltr.pl reads the TEnest output\nfile `my_input.LTR` and provides a vector graphic based picture of nested TEs in\nthe input sequence.\n\nThe svg_ltr.pl picture displays the original input sequence as a black line\nspanning the length of the display; however the annotated TEs have been removed\nfrom the sequence length. TE insertions are shown as triangles, their flat top\nrepresents their sequence length, and the bottom point represents the point of\nTE insertion. Therefore, a summation of all horizontal lines including the black\ninput sequence and all triangle tops would equal the length of the input\nsequence. LTR retrotransposons triangles have the LTRs shown with arrows at the\ntriangle top and have age since insertion shown in an internal box. A legend at\nthe bottom of the picture relates background triangle color to each displayed TE\nname.\n\nThe basic command to run svg_ltr.pl is `svg_ltr.pl my_input.LTR [options]`. This\nwill produce the scalable vector graphics (SVG) format picture my_input.svg.\nMany options are available for manipulating the TEnest graphic including subset\nviews, displaying specific annotation types, and adding third-party annotations\nto the picture.\n\n## Mapping Options\n\n- `--map_pair` Include pair classified LTR retrotransposons. T/F [T]\n\n- `--map_solo` Include solo classified LTRs. T/F [T]\n\n- `--map_nltr` Include non-LTR classified TEs. T/F [T]\n\n- `--map_frag` Include fragmented TE annotations. T/F [T]\n\n- `--map_gene` Include third-party gene annotations. Gene annotations can be\n  appended to the TEnest output file prior to running svg_ltr.pl. Similar to the\n  description of the TEnest output file above, each gene entry has a first line\n  in the form `GENE g0 F the gene name`, where 'g0' is a unique count identifier\n  for this gene, 'F' is the gene direction and any additional entries in the\n  line will be treated as the gene name. The second gene line contains the\n  annotation coordinates in the form `g0 1001 1100 1 100 1501 1600 101 200`,\n  groups of four coordinates representing exons with input sequence based start\n  and stop positions and gene based start and stop positions. T/F [T]\n\n- `--map_psdo` Include third-party pseudogene annotations. Similar to the\n  --map_gene option above, but substitute PSDO for GENE and u0 for g0. T/F [T]\n\n## Coordinate Options\n\n- `--print_coords` Print coordinates on displayed annotations. Coordinates can\n  be input sequence or TE based. A 'F' entry overrides the individual coordinate\n  options below, a 'SEQ' or 'TE' entry then checks the individual coordinate\n  option. F/SEQ/TE [F]\n\n- `--pair_coords` Display pair classified coordinates. T/F [T]\n\n- `--solo_coords` Display solo classified LTRs. T/F [T] --nltr_coords Display\n  non-LTR classified TEs. T/F [T]\n\n- `--frag_coords` Display fragmented TE coordinates. T/F [T]\n\n- `--gene_coords` Display third-party gene coordinates. T/F [T]\n\n- `--psdo_coords` Display third-party pseudogene coordinates. T/F [T]\n\n## Display Options\n\n- `--white_out` Draw white triangles within TE triangles for un-identified\n  regions. T/F [T]\n\n- `--age` Display MYA or BSR inside LTR retrotransposons. mya/bsr [mya]\n\n- `--start` Trim the display to this starting position. Any annotations prior to\n  this position will be ignored. []\n\n- `--end` Trim the display to this end position. Any annotations found after\n  this position will be ignored. []\n\n- `--split` If --start or --end are used the coordinates may sever a TE\n  annotation. T will trim the TE annotation and display the viewable fragment. F\n  will not display any portion of the TE. T/F [T] SVG format pictures can be\n  displayed directly in Mozilla Firefox version 2 or later\n  (http://www.mozilla.com/firefox). The linux program rsvg\n  (http://librsvg.sourceforge.net) is a convenient way to convert SVG files to\n  png or jpeg format pictures. The command\n  `rsvg --h 1000 my_input.svg my_input.png` will produce a publication quality\n  image.\n\n# Footnote\n\n### Background\n\nI (@cmdcolin) downloaded TEnest from the internet archive and am rehosting it on\ngithub for posterity. The plantGDB cgi-bin instance is no longer alive, and I\nthought that this tool makes such unique visualizations, that it deserved to be\nkept alive\n\nSoftware link\nhttps://web.archive.org/web/20150806130046/http://www.public.iastate.edu/~imagefpc/Subpages/software.html\n\nDownloaded from\nhttps://web.archive.org/web/20150806130046/http://www.public.iastate.edu/~imagefpc/Subpages/te_nest.html\n\nOriginal source code\nhttps://web.archive.org/web/20150806130046/http://www.public.iastate.edu/~imagefpc/Subpages/TE_nest/TEnest_scripts.tar.gz\n\nI believe this is TEnest v2, downloaded from a 2015 archive.org link.\n\n### License\n\nAs far as I (@cmdcolin) knows, there is no license attached to the source code\n\n### Concerns\n\nI am just hosting this for software historical purposes. If you wish for this\nrepository to be taken down, contact me and I will do so!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Ftenest","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmdcolin%2Ftenest","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Ftenest/lists"}