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new file mode 100644
index 0000000..4de8dd6
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+++ b/rust/tagfinder/Cargo.lock
@@ -0,0 +1,237 @@
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diff --git a/rust/tagfinder/Cargo.toml b/rust/tagfinder/Cargo.toml
new file mode 100644
index 0000000..97eff0f
--- /dev/null
+++ b/rust/tagfinder/Cargo.toml
@@ -0,0 +1,7 @@
+[package]
+name = "tagfinder"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+clap = { version = "4.5.20", features = ["derive"] }
diff --git a/rust/tagfinder/Makefile b/rust/tagfinder/Makefile
new file mode 100644
index 0000000..34892ff
--- /dev/null
+++ b/rust/tagfinder/Makefile
@@ -0,0 +1,2 @@
+run:
+	cargo run -- --families test/samples/families.tsv --positions test/samples/position.tsv --definitions 0,1
\ No newline at end of file
diff --git a/rust/tagfinder/src/finder.rs b/rust/tagfinder/src/finder.rs
new file mode 100644
index 0000000..f7fa48c
--- /dev/null
+++ b/rust/tagfinder/src/finder.rs
@@ -0,0 +1,135 @@
+use std::cmp::Ordering;
+use std::collections::HashMap;
+use std::fs::File;
+use std::io::{self, BufRead};
+use std::path::Path;
+
+fn read_lines<P>(filename: P) -> io::Result<io::Lines<io::BufReader<File>>>
+where
+    P: AsRef<Path>,
+{
+    let file = File::open(filename)?;
+    Ok(io::BufReader::new(file).lines())
+}
+
+pub fn parse_families<P>(filename: P) -> HashMap<String, u64>
+where
+    P: AsRef<Path>,
+{
+    let mut map: HashMap<String, u64> = HashMap::new();
+    if let Ok(lines) = read_lines(filename) {
+        for line in lines.flatten() {
+            let parts: Vec<&str> = line.split("\t").collect();
+            let gene = parts[0];
+            let family: u64 = parts[1].parse().unwrap();
+            map.insert(gene.to_string(), family);
+        }
+    }
+    map
+}
+
+pub fn parse_position<P>(filename: P) -> Vec<(String, String, u64, u64)>
+where
+    P: AsRef<Path>,
+{
+    let mut vec: Vec<(String, String, u64, u64)> = Vec::new();
+    if let Ok(lines) = read_lines(filename) {
+        for line in lines.flatten() {
+            let parts: Vec<&str> = line.split("\t").collect();
+            let gene = parts[0];
+            let chromosome = parts[1];
+            let start: u64 = parts[2].parse().unwrap();
+            let end: u64 = parts[3].parse().unwrap();
+            vec.push((gene.to_string(), chromosome.to_string(), start, end));
+        }
+    }
+    vec
+}
+
+pub fn compare_gene_position(
+    position_a: &(String, String, u64, u64),
+    position_b: &(String, String, u64, u64),
+) -> Ordering {
+    let (_gene_a, chromosome_a, start_a, _end_b) = position_a;
+    let (_gene_b, chromosome_b, start_b, _end_b) = position_b;
+    if chromosome_a < chromosome_b {
+        return Ordering::Less;
+    } else if chromosome_a > chromosome_b {
+        return Ordering::Greater;
+    } else {
+        if start_a < start_b {
+            return Ordering::Less;
+        } else {
+            return Ordering::Greater;
+        }
+    }
+}
+
+pub fn detect_tag_of_definitions(
+    definitions: &Vec<u64>,
+    gene_positions: &Vec<(String, String, u64, u64)>,
+    gene_families: &HashMap<String, u64>,
+) -> HashMap<String, (String, Vec<Option<u64>>)> {
+    let mut tag_numbers: HashMap<String, (String, Vec<Option<u64>>)> = HashMap::new();
+    for definition in definitions {
+        let tag_numbers_def = detect_tag_of_definition(*definition, gene_positions, gene_families);
+        for (gene, (family, tag)) in tag_numbers_def {
+            if tag_numbers.contains_key(&gene) {
+                let (_gene, tags) = tag_numbers.get_mut(&gene).unwrap();
+                tags.push(tag);
+            } else {
+                tag_numbers.insert(gene, (family, vec![tag]));
+            }
+        }
+    }
+    tag_numbers
+}
+
+pub fn detect_tag_of_definition(
+    definition: u64,
+    gene_positions: &Vec<(String, String, u64, u64)>,
+    gene_families: &HashMap<String, u64>,
+) -> HashMap<String, (String, Option<u64>)> {
+    let mut tag_numbers: HashMap<String, (String, Option<u64>)> = HashMap::new();
+    let mut spacer_index: u64 = 0;
+    let mut tag_index: u64 = 0;
+    for (i, (gene_i, chromosome_i, _start_i, _end_i)) in gene_positions.iter().enumerate() {
+        let family_repr: String;
+        let mut is_on_tag: bool = false;
+        if let Some(family_i) = gene_families.get(gene_i) {
+            family_repr = format!("{}", family_i);
+            let mut nb_intra_tag_spacers: u64 = 0;
+            if !tag_numbers.contains_key(gene_i) {
+                for (gene_j, chromosome_j, _start_j, _end_j) in &gene_positions[(i + 1)..] {
+                    if *chromosome_i != *chromosome_j {
+                        break;
+                    }
+                    if let Some(family_j) = gene_families.get(gene_j) {
+                        if *family_i == *family_j {
+                            nb_intra_tag_spacers = 0;
+                            if !is_on_tag {
+                                is_on_tag = true;
+                                tag_index += 1;
+                                tag_numbers.insert(gene_i.clone(), (family_repr.clone(), Some(tag_index)));
+                            }
+                            tag_numbers.insert(gene_j.clone(), (family_repr.clone(), Some(tag_index)));
+                        }
+                    } else {
+                        nb_intra_tag_spacers += 1;
+                    }
+                    if nb_intra_tag_spacers > definition {
+                        break;
+                    }
+                }
+                if !is_on_tag {
+                    tag_numbers.insert(gene_i.clone(), (family_repr, None));
+                }
+            }
+        } else {
+            spacer_index += 1;
+            family_repr = format!("spacer{}", spacer_index);
+            tag_numbers.insert(gene_i.clone(), (family_repr, None));
+        }
+    }
+    tag_numbers
+}
diff --git a/rust/tagfinder/src/main.rs b/rust/tagfinder/src/main.rs
new file mode 100644
index 0000000..73a7068
--- /dev/null
+++ b/rust/tagfinder/src/main.rs
@@ -0,0 +1,57 @@
+use std::{collections::HashMap, path::PathBuf};
+use clap::Parser;
+use finder::{detect_tag_of_definitions, parse_families, parse_position};
+
+mod finder;
+
+#[derive(Parser)]
+#[command(version="0.0.1", about="Find Tandemly Arrayed Genes", long_about="Find Tandemly Arrayed Genes in a genome based on gene position and Tandemly Arrayed Genes definition (i. e. number of spacers)")]
+struct Cli {
+    #[arg(short='f', long="families", value_name="FAMILIES FILE")]
+    families: PathBuf,
+    
+    #[arg(short='p', long="positions", value_name="POSITIONS FILE")]
+    positions: PathBuf,
+
+    #[arg(short='d', long="definitions", value_name="TAGs DEFINITIONS", help="Comma seperated integers for the number of spacers to consider")]
+    definitions: String
+}
+
+fn main() {
+    let cli = Cli::parse();
+
+    let gene_families: HashMap<String, u64> = parse_families(cli.families);
+
+    let mut gene_positions: Vec<(String, String, u64, u64)> = parse_position(cli.positions);
+
+    gene_positions.sort_by(|a, b | crate::finder::compare_gene_position(a, b));
+
+    let definitions: Vec<u64> = cli.definitions.split(",").map(|x| x.parse().unwrap()).collect();
+
+    let tag_numbers = detect_tag_of_definitions(&definitions, &gene_positions, &gene_families);
+
+    // Print header
+    print!("gene\tfamily\t");
+    for (i, definition) in definitions.iter().enumerate() {
+        print!("tag{}", definition);
+        if (i + 1) < definitions.len() {
+            print!("\t");
+        }
+    }
+    print!("\n");
+    
+    for (gene, (family, tags)) in tag_numbers {
+        print!("{}\t{}\t", gene, family);
+        for (i, tag) in tags.iter().enumerate() {
+            if let Some(tag) = tag {
+                print!("{}", tag);
+            } else {
+                print!("-");
+            }
+            if (i + 1) < tags.len() {
+                print!("\t");
+            }
+        }
+        print!("\n");
+    }
+}
diff --git a/rust/tagfinder/test/samples/families.tsv b/rust/tagfinder/test/samples/families.tsv
new file mode 100644
index 0000000..8d12e15
--- /dev/null
+++ b/rust/tagfinder/test/samples/families.tsv
@@ -0,0 +1,4 @@
+A	1
+B	1
+C	2
+D	2
diff --git a/rust/tagfinder/test/samples/position.tsv b/rust/tagfinder/test/samples/position.tsv
new file mode 100644
index 0000000..7f9e0c0
--- /dev/null
+++ b/rust/tagfinder/test/samples/position.tsv
@@ -0,0 +1,6 @@
+A	1	1	1
+B	1	2	1
+C	2	3	1
+U	2	4	1
+V	2	5	1
+D	2	10	1
\ No newline at end of file